Upper Penitencia Creek Limiting Factors Analysis Final Technical

Transcription

Upper Penitencia Creek
Limiting Factors Analysis
Final Technical Report
Prepared for
Santa Clara Valley
Urban Runoff
Pollution Prevention Program
(Program Manager, EOA, Inc.)
1410 Jackson Street
Oakland, CA 94612
Prepared by
Stillwater Sciences
2855 Telegraph Avenue, Suite 400
Berkeley, CA 94705
18 August 2006
FINAL TECHNICAL REPORT
Upper Penitencia Creek Limiting Factors Analysis
EXECUTIVE SUMMARY
The Santa Clara Valley Urban Runoff Pollution Prevention Program (SCVURPPP) developed a
Work Plan for Conducting a Watershed Analysis and Management Practice Assessment in Other
Creeks Potentially Impaired by Sediment from Anthropogenic Activities (Work Plan) in
fulfillment of the SCVURPPP NPDES Permit Order No. 01-024 Provision C.9.f.iii paragraph 2.
The SCVURPPP contracted with Stillwater Sciences to complete Task 1 of the Work Plan,
Conduct Watershed Assessment using Limiting Factor Analysis (LFA) Approach, in the Upper
Penitencia Creek watershed.
The objectives of the Upper Penitencia Steelhead LFA were to identify and fill information gaps
related to physical and biological factors controlling population dynamics of steelhead
(Oncorhynchus mykiss) and to identify the impacts of sediment on steelhead relative to other
potential limiting factors. Based on the available existing information and reconnaissance
surveys, focused studies were developed to test hypotheses regarding potential limiting factors for
steelhead in the Upper Penitencia Creek watershed. The focused studies addressed the following
factors: fish passage barriers, gravel permeability, pool filling, overwintering habitat, and summer
rearing and growth.
A summary of the findings of the Upper Penitencia Creek LFA includes:
1. No barriers to upstream migration below natural waterfalls in Upper Penitencia Creek
and Arroyo Aguague were identified, although a passage impediment in Alum Rock Park
may limit passage opportunities at some flow levels;
2. Seasonal low flows in the downstream reaches may limit steelhead outmigration success
in some years, especially if channel drying occurs before the end of the outmigration
period (typically March–May);
3. Gravel permeability is low but not likely limiting smolt production due to habitat
limitations at other life stages;
4. Pool filling is low, indicating high transport capacity of fine sediment relative to supply;
5. Preliminary analysis suggests that overwintering habitat is likely the key limiting factor
for steelhead prior to smolt outmigration;
6. Potential limitations to steelhead density and fish growth may exist in Upper Penitencia
Creek due to low streamflows and warm water temperatures during the summer period.
These findings indicate that factors associated with juvenile rearing, especially winter habitat
conditions, are likely to have the greatest influence on the steelhead population. Sediment
dynamics in Upper Penitencia Creek are directly related to juvenile rearing capacities by the
embedding of coarse substrate such as cobble and boulders. However, existing information is not
sufficient to differentiate current anthropogenic sediment inputs from what is likely a naturally
high sediment yield from the watershed. Additional uncertainty remains regarding the potential
effects on smolt production of seasonal low flows and elevated water temperatures during the
outmigration and summer rearing periods. Important data gaps and information needs were
identified to reduce uncertainty associated with development and testing of the key hypotheses
investigated in this study. The recommendations for additional studies presented at the end of this
report may be facilitated and their effectiveness enhanced through coordination with existing
and/or proposed programs.
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Table of Contents
EXECUTIVE SUMMARY .............................................................................................................i
1
INTRODUCTION AND APPROACH............................................................................1
1.1
Introduction ............................................................................................................1
1.2
Analysis Approach .................................................................................................2
2
WATERSHED CHARACTERIZATION .......................................................................4
2.1
Physical Setting ......................................................................................................4
2.2
Climate and Hydrology ..........................................................................................4
2.3
Land Use and Land Cover......................................................................................6
2.4
Geologic Setting .....................................................................................................7
2.4.1 Santa Clara Basin .....................................................................................7
2.4.2 Upper Penitencia Creek ............................................................................8
2.4.3 Landslides .................................................................................................9
2.5
Geomorphic Setting..............................................................................................10
2.5.1 Overview..................................................................................................10
2.5.2 General Description................................................................................11
2.5.3 Disturbance Factors................................................................................12
2.5.4 Current Condition by Study Reach..........................................................13
2.6
Fish Community Composition .............................................................................17
3
ANALYSIS SPECIES .....................................................................................................19
3.1
Steelhead Status and Life History Overview........................................................19
3.2
Steelhead Life History and Habitat Use Conceptual Model.................................21
3.3
Conceptual Model ................................................................................................21
4
FOCUSED STUDIES......................................................................................................25
4.1
O. mykiss Abundance ...........................................................................................25
4.1.1 Population Assessment............................................................................25
4.1.2 Population Modeling...............................................................................28
4.2
Changes in Physical Habitat.................................................................................29
4.3
Sediment-Related Impacts on Salmonid Habitat..................................................32
4.3.1 Spawning Gravel .....................................................................................33
4.3.2 Pool Filling and Juvenile Rearing Habitat .............................................36
4.3.3 Winter Habitat Suitability .......................................................................38
4.4
Fish Passage Barriers............................................................................................42
4.4.1 Structural Fish Passage Barriers............................................................43
4.4.2 Flow-related Barriers .............................................................................47
4.5
O. mykiss Growth .................................................................................................50
5
LIMITING FACTORS SYNTHESIS............................................................................53
6
CONCLUSIONS AND PROPOSED ACTIONS ..........................................................58
7
LITERATURE CITED...................................................................................................64
APPENDIX A ............................................................................................................................ A-1
APPENDIX B..............................................................................................................................B-1
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List of Tables
Table 2-1. Areal extent of land use/land cover types in the Upper Penitencia Creek Watershed... 6
Table 2-2. Geologic units in the Upper Penitencia Creek Basin. ................................................... 9
Table 2-3. Reaches of Upper Penitencia Creek developed for this report and derived from other
sources. .......................................................................................................................................... 13
Table 4-1. Linear feet of modified and unmodified stream channel in Upper Penitencia Creek
(excluding Alum Rock Park)......................................................................................................... 32
Table 4-2. Linear feet of modified and unmodified stream channel in Alum Rock Park............. 32
Table 4-3. Number of potential spawning gravel patches greater than or equal to various size
classes in Upper Penitencia Creek upstream of RM 3.5................................................................ 35
Table 4-4. Pool characteristics of selected streams in the Santa Clara Valley. ............................ 38
Table 4-5. Winter 0+ juvenile steelhead density (fish/ft2) in an artificial stream channel with
different levels of coarse substrate embeddedness. ....................................................................... 40
Table 4-6. Documented fish passage impediments and barriers in Upper Penitencia Creek, up to
and including the natural waterfall. ............................................................................................... 44
Table 4-7. Measured characteristics of the grade control drop structure located at the Youth
Science Institute in Alum Rock Park (GB18). .............................................................................. 45
Table 4-8. Location of Upper Penitencia Creek temperature data loggers. .................................. 52
Table 5-1. Summary of conceptual models and hypotheses regarding historical and current
conditions in the Upper Penitencia Creek watershed and their potential effects on different life
stages of steelhead. ........................................................................................................................ 55
Table 6-1. Summary of conclusions and recommended studies.................................................. 59
List of Figures
Figure 2-1.
Figure 2-2.
Figure 2-3.
Figure 3-1.
Figure 3-2.
Figure 4-1.
Figure 4-2.
Figure 4-3.
Figure 4-4.
Figure 4-5.
Monthly mean temperature and precipitation in Mount Hamilton, CA, and San
Jose, CA, average from 1948-2004.
Mean daily streamflow in Upper Penitencia Creek at SCVWD gage SF 83 at Dorel
Drive, Water Years 1962-2004.
Upper Penitencia Creek land use comparison between years 1939, 1960, and 2004.
(Scale 1 inch= 0.195 miles).
Natural fish passage barriers: waterfalls in Arroyo Aguague (left) and Upper
Penitencia Creek (right).
Steelhead and resident rainbow trout life cycle and potential limiting factors in the
Upper Penitencia Creek watershed.
Spring and Fall 2005 densities for 0+ O. mykiss in Upper Penitencia Creek and
Arroyo Aguague.
Spring and Fall 2005 densities for 1+ and 2+ O. mykiss in Upper Penitencia Creek
and Arroyo Aguague.
Spring and Fall 2005 population estimates for 0+ O. mykiss in Upper Penitencia
Creek and Arroyo Aguague.
Spring and Fall 2005 population estimates for 1+ and 2+ O. mykiss in Upper
Penitencia Creek and Arroyo Aguague.
Length frequency histograms for steelhead in Upper Penitencia Creek in 1997 (A),
and from outmigrant traps in Coyote Creek during 1998 (B), 1999 (C), and 2000
(D).
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Figure 4-6.
Figure 4-7.
Figure 4-8.
Figure 4-9.
Figure 4-10.
Figure 4-11.
Figure 4-12.
Figure 4-13.
Figure 4-14.
Figure 4-15.
Figure 4-16.
Figure 4-17.
Figure 4-18.
Figure 4-19.
Figure 4-20.
Upper Penitencia Creek stream channel comparison between years 1873, 1899, and
1951 (Scale 1 inch= 0.663 miles). Historical maps courtesy of San Francisco
Estuary Institute, Historical Ecology Program.
The egg survival-to-emergence index used to interpret the relative impact of
measured permeability on steelhead production is based on the regression derived
from data collected by Tagart (1976) for coho salmon and McCuddin (1977) for
Chinook salmon.
Expected potential smolt production as a function of emergence survival.
Area (ft²) of spawning gravel, summed over 0.1 mi increments upstream from the
mouth of Upper Penitencia Creek (includes both Upper Penitencia Creek and
Arroyo Aguague data).
Predicted survival to emergence at permeability sites in Upper Penitencia Creek
and Arroyo Aguague.
Predicted median survival to emergence, with 95% confidence intervals, for
sampled reaches in Upper Penitencia Creek and Arroyo Aguague.
Pool filling in Upper Penitencia Creek and Arroyo Aguague. Values < 10% should
be interpreted as low in basins with fines-rich parent material, values of 10-20% are
moderate, and > 20% are high (Lisle and Hilton 1999, Kondolf et al. 2003).
Median V-star (pool filling) values, with 95% confidence intervals, for sampled
reaches in Upper Penitencia Creek and Arroyo Aguague.
Boulder and cobble substrate composition, summed over 0.1 mile increments
upstream from the mouth of Upper Penitencia Creek (includes both Upper
Penitencia Creek and Arroyo Aguague data).
Expected smolt production as a function of overwintering habitat quality (i.e., fish
density).
Grade control weir at Youth Science Institute in Alum Rock Park. Flow at Dorel
gage at time of photo = 0.51 cfs.
Steelhead leaping ability curves, with YSI grade control weir dimensions
superimposed.
Cumulative percentage of spawning gravel area, pool area, and cobble/boulder
substrate area in Upper Penitencia Creek upstream of RM 3.5 (includes both Upper
Penitencia Creek and Arroyo Aguague data).
Daily average stream temperatures at monitoring locations in Upper Penitencia
Creek in 2000 (A) and 2001 (B), with available streamflow data.
Daily average stream temperatures at monitoring locations in Upper Penitencia
Creek in 2002 (C) and 2004 (D), with available streamflow data.
List of Maps
Map 1. Base Map
Map 2. Land Use/Land Cover Map
Map 3. Geologic Map
Map 4. Focused Field Studies Map
List of Appendices
Appendix A-1: Steelhead Population Estimation
Appendix A-2: Steelhead Population Dynamics Modeling
Appendix A-3: Spawning Gravel Permeability
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Appendix A-4: Pool Filling
Appendix A-5: Overwintering Habitat
Appendix A-6: Fish Passage Barriers
Appendix A-7: Available Water Temperature Data for Upper Penitencia Creek
Appendix B: Steelhead Species Summary
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1
INTRODUCTION AND APPROACH
1.1
Introduction
This report presents the results of studies and information synthesis conducted by Stillwater
Sciences to analyze factors potentially limiting the steelhead (Oncorhynchus mykiss) population
in Upper Penitencia Creek, in Santa Clara County, California. This study was funded by the Santa
Clara Valley Urban Runoff Pollution Prevention Program (SCVURPPP), as part of SCVURPPP’s
efforts to assess sediment-related impacts to beneficial uses in Upper Penitencia Creek and other
streams in the Santa Clara Valley. Upper Penitencia Creek is among the streams previously
identified by SCVURPPP as high priority for watershed analysis due to the potential for
anthropogenic sediment impairment.
SCVURPPP developed a Work Plan for Conducting a Watershed Analysis and Management
Practice Assessment in Other Creeks Potentially Impaired by Sediment from Anthropogenic
Activities (Work Plan) in fulfillment of the SCVURPPP NPDES Permit Order No. 01-024
Provision C.9.f.iii paragraph 2. This study was conducted to complete Task1 of the Work Plan for
Upper Penitencia Creek, which was to “Conduct Watershed Assessment using Limiting Factor
Analysis Approach.” The Work Plan identifies four major objectives for the watershed analysis:
•
•
•
•
Collect available existing data to characterize the watershed and identify issues of
concern;
Develop hypotheses to understand potential impacts of sediment to species that are
sensitive to excess sediment;
Conduct focused studies to test hypotheses; and
Implement a limiting factors analysis to determine to what degree human-related
sediment impacts are key limiting factors for aquatic species of concern.
Task 2 of the Work Plan, Assess Sediment Management Practices, will be conducted in FY 05-06
by the SCVURPPP, subsequent to the completion of the LFA. An additional objective of the
Work Plan is to conduct a rapid sediment budget for Upper Penitencia Creek (Task 4) in FY 05–
06 if the results of the watershed analysis indicate excessive sediment production from
anthropogenic activities are impairing aquatic life uses.
In response to the four SCVURPPP analysis objectives listed above, the primary focus of this
study was to characterize the nature and degree of potential sediment-related effects on steelhead.
Steelhead is the species previously identified by SCVURPPP as the target for focused study based
on its presence in Upper Penitencia Creek and its sensitivity to sediment-related impacts.
Although this analysis primarily considered sediment and its potential impacts on habitat
suitability for steelhead, we recognize the importance of other watershed impacts, their influence
on watershed processes, and their potential effects on a variety of aquatic organisms (e.g.,
amphibians) and ecosystem functions. Our study approach therefore included an investigation of
additional factors to provide a broader context for evaluating the effects of management actions in
the Upper Penitencia Creek watershed, and for providing scientifically-based restoration and
management recommendations.
This study was designed to provide an assessment of current conditions from a watershed-wide
perspective and, using an iterative process of hypothesis development and testing, to identify the
factors that are most likely limiting the population of steelhead in Upper Penitencia Creek. The
study also included a limited effort to reconstruct historical conditions using available
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information to document changes that have occurred in stream habitat conditions, particularly
those most likely to affect steelhead. This limited historical analysis was intended to improve our
interpretation of current conditions, the nature and degree of water quality impairment by
sediment and other factors, and generate and test hypotheses to guide management and future
study. The scope and timeframe of this study were not sufficient, however, to support the more
intensive sampling and analysis program that would be required to perform a more
comprehensive assessment of historical and current conditions. Also, it should be noted that the
water quality portion of our analysis was focused on sediment and temperature as potential
limiting factors. Other water quality parameters, such as nutrients, pathogens, or chemical
contaminants may affect steelhead or other beneficial uses, but our initial evaluation of existing
data indicated that these parameters are not problematic in Upper Penitencia Creek.
The watershed’s extensive land use history for agricultural, recreational, and urban uses (see
Sections 2.3 and 4.2), and existing population of steelhead (see Sections 2.6 and 4.1) make it an
important watershed in which to focus studies that investigate the potential impacts of
anthropogenic sources of sediment on aquatic life. Our area of study encompassed the Upper
Penitencia Creek drainage upstream from the confluence with Coyote Creek. Focused analyses,
however, were concentrated in the reach upstream of Noble Avenue (approximately 3.5 miles
upstream of the Coyote Creek confluence), since this is the portion of the creek documented to
support steelhead and was previously described as the primary zone of steelhead spawning and
rearing (Smith 1998, Li 2001, BRG 2001).
1.2
Analysis Approach
Our approach was to explore factors potentially limiting steelhead production to determine
possible causes of current adverse impacts or historical decline. By identifying these factors, we
can focus future management activities, help prioritize actions, and refine our current
understanding of the ecosystem. Hypotheses regarding potential limiting factors for steelhead
were developed using a conceptual model that describes steelhead life history and identifies the
habitat constraints most likely to affect the success of each life stage. We then used an iterative
process of hypothesis development, testing, and refinement to provide the most adaptive and
effective mechanism possible for identification of priority management actions in the Upper
Penitencia Creek watershed. This approach mirrors that used by Stillwater Sciences for the 2004
Stevens Creek Limiting Factors Analysis, and both are based in part on a similar study conducted
by Stillwater Sciences and UC Berkeley for the Napa River watershed (Napa County) (Stillwater
Sciences and Dietrich 2002). Similar approaches are currently being used in other Bay Area
watersheds, including Lagunitas Creek (Marin County) and Sonoma Creek (Sonoma County).
The Limiting Factors Analysis was a five-step process:
Step 1. Assemble and Review Available Information. We assembled and reviewed relevant
existing information and queried local experts to characterize the general physical and biological
attributes of the Upper Penitencia Creek watershed and identify key issues of concern. This step
included development of various Geographic Information System (GIS) layers that reflected
watershed conditions in a map-based format and allowed us to stratify the watershed and channel
network to aid in hypothesis development and study site selection.
Step 2. Develop and Refine Conceptual Model, Hypotheses, and Work Plan for Focused
Studies. Building on the watershed characterization and other information developed in Step 1,
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we developed and refined a conceptual model that describes the habitat requirements and
potential constraints for each steelhead life stage in Upper Penitencia Creek. Based on our
conceptual model and existing information, we began developing hypotheses regarding current
habitat conditions and potential limiting factors for steelhead. We then conducted initial
reconnaissance of the watershed to begin refining hypotheses and identify priorities for focused
studies. Sections 3 and 4 of this report describe the results of Step 2.
Step 3. Conduct Focused Studies. We conducted focused studies to begin testing the most likely
hypotheses. We also assessed the uncertainty associated with the results of the focused studies.
Focused studies included review and synthesis of available information on aquatic habitat, land
use, potential fish passage barriers, and water temperature, as well as field assessment of
spawning gravel permeability, pool filling, overwintering habitat suitability, channel
geomorphology, and steelhead distribution and abundance (via direct observation [snorkel]
surveys). The results of focused studies led, in some cases, to development of new hypotheses
and additional field studies. Section 4 describes the results of the focused studies conducted for
this analysis. More detailed methods and data for the focused studies are provided in Appendix A.
Step 4. Conduct Limiting Factors Analysis. This step involved review and synthesis of
available data from the focused studies and other sources to evaluate the factors most likely to be
limiting populations of steelhead under current conditions. Steelhead population response
modeling was used as an important tool in the synthesis. This analysis of limiting factors helped
provide the context for rejecting, accepting, or refining hypotheses based on the results of the
focused studies, and improved our understanding of key uncertainties that might affect
management of aquatic ecosystems in the watershed. The results of the limiting factors analysis
are discussed throughout Section 5 and summarized in Section 6.
Step 5. Develop Recommendations. Based on information currently available and information
and hypotheses developed during these studies, we identified management actions and priorities
and developed recommendations for future studies to establish cause-and-effect relationships
between limiting factors and human land use activities. Our preliminary recommendations are
summarized in Section 7.
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2
WATERSHED CHARACTERIZATION
This section provides a general description of the Upper Penitencia Creek watershed based on an
initial review of available information, GIS analysis, and reconnaissance surveys. This watershed
characterization provides the foundation for subsequent identification of potential limiting factors
and development of initial hypotheses and focused studies to begin testing key hypotheses.
2.1
Physical Setting
Upper Penitencia Creek drains a watershed of approximately 24 mi2 (SCBWMI 2001) (Map 1).
Included in this drainage is the 9 mi2 (23 km2) watershed of Arroyo Aguague, the major tributary
to Upper Penitencia Creek. Upper Penitencia Creek originates at an elevation of 3,150 feet (960
meters) in the Diablo Range just east of San Jose, flowing westward for 2.5 miles (4 kilometers)
before reaching Cherry Flat Reservoir. The creek flows westward for another nine miles (14.5
kilometers) through Alum Rock Park, Penitencia Creek County Park, and across the alluvial plain
through the city of San Jose. Upper Penitencia Creek joins Coyote Creek about ½ mile (0.8
kilometers) east of the intersection of Berryessa Road and Highway 101. Downstream of the
confluence of Coyote and Upper Penitencia Creeks, Coyote Creek continues north for ten miles
(16 kilometers) to South San Francisco Bay. The Upper Penitencia watershed is bordered by the
Lower Penitencia Creek watershed to the north and the Silver Creek watershed to the south.
2.2
Climate and Hydrology
The Santa Clara Valley is dominated by a Mediterranean climate with warm, dry summers and
cool, moist winters. The majority of annual precipitation occurs as rainfall in the winter and early
spring (Figure 2-1). The amount of precipitation in the Upper Penitencia Creek watershed is
highly variable from year to year, and several droughts of 5–7 years have occurred within the
Santa Clara Valley Basin in historical times (SCBWMI 2001). Precipitation is heaviest in the
upper watershed (average of 23 inches [58 centimeters] per year) and decreases westward
towards San Jose (average of 14 inches [35 centimeters] per year) (data from 1948–2005,
Western Regional Climate Center 2005). Temperatures are generally cooler at Mount Hamilton
than in San Jose, with an average temperature difference of 7˚F (3.9˚C) (Western Regional
Climate Center 2005). From November through April, temperature within the watershed varies on
average by 9˚F (5˚C), from 45˚F (7.2˚C) on Mount Hamilton to 54˚F (12.2˚C) in San Jose. From
May though October, temperature between Mount Hamilton and San Jose varies less, with an
average variation of 4˚F (2.2˚C), from 62˚ (16.6˚C) F at Mount Hamilton to 66˚F (18.8˚C) in San
Jose.
Upper Penitencia Creek is perennial at its headwaters and becomes intermittent during dry years
once it reaches the floor of the Santa Clara Valley. Flow in the upper reaches of Upper Penitencia
Creek is mainly due to the contribution of water from natural springs and a perennial tributary,
Arroyo Aguague, which joins Upper Penitencia Creek at RM (river mile) 6.7 (6.7 miles upstream
from the confluence with Coyote Creek) (SCBWMI 2001). Arroyo Aguague provides the
majority of summer baseflow in the section of Upper Penitencia Creek that flows through Alum
Rock Park (SCVURPPP 2003a). In addition to Arroyo Aguague, six small tributaries feed into
Upper Penitencia Creek, however most are ephemeral. The springs and tributaries help sustain
summer baseflows of approximately 0.5 cfs through Alum Rock Park (BRG 2001).
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In addition to the influence of naturally occurring springs and tributaries, flow in Upper
Penitencia Creek is also affected by releases from Cherry Flat Dam (RM 9.0). Cherry Flat Dam
was constructed in 1936 in Upper Penitencia Creek upstream of Alum Rock Park at an elevation
of 1,700 ft (518 m) and is owned and operated by the City of San Jose (BRG 2001, EOA 2003).
The reservoir drains 2.4 mi² (6.2 km2), has a capacity of 500 acre-feet and was originally built for
flood control and to maintain perennial flow within the park (BRG 2001, SCBWMI 2001 and
2003). The current capacity of the reservoir is likely much less than 500 acre-feet, and may not be
large enough to provide significant flood protection (J. Abel, SCVWD, pers. comm., 2006). Forty
years after construction, Alum Rock Park began using municipal water supply and the reservoir is
now used primarily for flood control, with releases made only during years when the reservoir is
in danger of exceeding capacity or when additional flows are needed to maintain perennial flow
in the main channel of Upper Penitencia Creek (SCVURPPP 2003a). Periodic flow augmentation
downstream of Cherry Flat Dam is believed to have increased the extent and duration of wetted
habitat in Alum Rock Park during summer, but the exact amount of habitat gained and the effects
of this increase on steelhead production are unknown. Regular releases from the dam are not
required in most years due to the contribution of natural springs near the dam and the perennial
flow from Arroyo Aguague (SCVURPPP 2003a).
Streamflow in the downstream, valley floor reach is also affected by water diversions and the
operation of off-channel percolation ponds. Intermittent streamflow is believed to be a natural
occurrence downstream of Alum Rock Park (R. Grossinger, San Francisco Estuary Institute, pers.
comm., 2005); however the operation of the percolation ponds near Noble Avenue (RM 3.6) and
Mabury Road (RM 1.3) has altered natural flow patterns (Buchan et al. 1999). At Noble Avenue,
water from the main channel of Upper Penitencia Creek is diverted into three off-channel
percolation ponds that are operated by the Santa Clara Valley Water District (SCVURPPP 2003a,
SCBWMI 2003). Diversions typically occur from April–October, and the percolation ponds are
operated year-round (J. Abel, SCVWD, pers. comm., 2006). This water, along with water
imported from the South Bay Aqueduct, is used for groundwater recharge and re-enters the main
channel for instream percolation, augmenting stream flow for almost two miles (3.2 kilometers)
downstream of the ponds (Buchan et al. 1999). Further downstream near Mabury Road, water is
diverted to another percolation pond, which then re-enters the main channel just downstream. The
Mabury diversion is operated under a water right for streamflow diversion from November–May,
and may be operated at other times of the year for diversion of water from the South Bay
Aqueduct delivered via the stream (J. Abel, SCVWD, pers. comm., 2006). Although the
percolation ponds are created for groundwater recharge, the water diversion can cause drying of
the channel downstream of Mabury Road from late spring to early fall (SCVURPPP 2003a). Flow
in Upper Penitencia Creek was not monitored before the construction of either Cherry Flat
Reservoir or the percolation ponds, so the effects of these impoundments on hydrology remain
unclear.
Two SCVWD hydrologic gages currently monitor flow in Upper Penitencia Creek. The most
upstream gage, SF 83, is located at Dorel Drive (RM 3.9), near the entrance to Alum Rock Park
(Map 1). It has recorded streamflow data since 1961 (Figure 2-2). The downstream gage, SF 87,
is located at RM 1.3, near Mabury Road. Stream flow data from SF 87 are available beginning in
water year 2004. Data from the Dorel gage (SF 83), illustrate the pattern of high winter and
spring flow peaks followed by periods of drastically lower, stable flows (typically <1 cfs)
throughout the summer and early fall.
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2.3
Land Use and Land Cover
In its upper reaches the Upper Penitencia Creek watershed is characterized by deep, narrow
canyons with well-developed riparian vegetation and few anthropogenic watershed disturbances
(SCBWMI 2001). The upper watershed is predominantly undeveloped open space, with only a
few residential houses (SCBWMI 2003) (Map 2). Almost three-fourths of the total forested area
in the watershed and half of the total rangeland area occur in the upper watershed upstream of the
confluence with Arroyo Aguague (Table 2-1). Forest continues to be the predominant land cover
type throughout Alum Rock Park (Map 2).
Table 2-1. Areal extent of land use/land cover types in the Upper Penitencia Creek Watershed.
Land Use/Cover Type
Agriculture
Commercial
Forest
Freshwater
Heavy Industrial
Light Industrial
Public/Quasi-Public
Rangeland
Residential, 1 to 3 DU/acre
Residential, 4+ DU/acre
Transportation, Communication
Urban Recreation
Vacant/Undeveloped
TOTAL1
Acres
164.9
89.7
10,010.1
31.7
74.5
62.6
37.9
3,643.9
53.0
1,248.9
26.6
21.9
39.3
15,505.0
mi2
0.3
0.1
15.7
0.1
0.1
0.1
0.1
5.7
0.1
2.0
0.0
0.0
0.1
24.2
km2
0.7
0.4
40.5
0.1
0.3
0.3
0.2
14.7
0.2
5.1
0.1
0.1
0.2
62.8
Total (%)
1.1
0.6
64.6
0.2
0.5
0.4
0.2
23.5
0.3
8.1
0.2
0.1
0.3
100.0
Source: SCBWMI 2001, land use in 1995
1
Because of differing data sources, these totals do not match those for geologic units reported in Section 2.4.
DU = Developed Unit(s)
Downstream of Alum Rock Park, Upper Penitencia Creek flows out of its steep canyon onto the
alluvial plains of San Jose. A narrow strip of trees flanks the main channel of Upper Penitencia
Creek, creating a riparian corridor that connects the Diablo Range to the Coyote Creek corridor
(SCBWMI 2001). Beyond the riparian corridor, urban land uses dominate. Residential
neighborhoods cover a large portion of the lower watershed, comprising over 8% of the total
watershed area. Here, housing is interspersed with agricultural uses, commercial uses, industrial
centers, and public developments, collectively covering 2.8% of the lower watershed.
Transportation, communication, urban recreation, vacant, undeveloped land, and freshwater
collectively cover less than 1% of the Upper Penitencia Creek Watershed (SCBWMI 2001).
By the late 1800s the Santa Clara Valley around Upper Penitencia Creek was already showing
signs of escalating urbanization (Hoffman 1873, USGS 1899). During the first several decades of
the 20th century, most undeveloped land around the creek was cultivated as orchards. Beginning
in the 1950s, orchard conversion to residential properties supported a burst of development that
continues to the present day (Figure 2-3). Orchards once lined the entire length of Upper
Penitencia Creek downstream of Alum Rock Park, but by the year 2000, most were replaced with
urban infrastructure and homes. Despite the rapid urban development in the lower watershed over
the past century, the upstream reaches of Upper Penitencia Creek remain relatively undeveloped.
Upstream of Alum Rock Park the basin is sparsely covered by homes, ranches, and private roads.
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6
Channel alterations have occurred continuously along Upper Penitencia Creek since European
settlement. Mineral baths made Alum Rock Park an extremely popular destination from the later
part of the 19th century through the first half of the 20th century. Many of the baths were located
adjacent to the creek within the riparian corridor, and banks were lined with rock walls to
accommodate and maintain their usage. The walls remain in place to this day, leaving a tightly
confined box channel. Downstream of the park, much of the channel presently flows under
several generations of streets, highways, power lines, and railroads. In addition, drop structures,
storm drains, bank revetment, and other features have been installed in the channel and along the
banks to route surface runoff and control erosion. Historical evidence shows that Upper
Penitencia Creek once flowed directly into the San Francisco Bay, but was diverted to join
Coyote Creek in the mid-1870s (see Section 4.2).
These changes in land use, flow regulation and routing, and channel condition have affected the
physical processes that influence the quality, abundance, and connectivity of habitat for
anadromous fish and aquatic and riparian species in Upper Penitencia Creek.
2.4
2.4.1
Geologic Setting
Santa Clara Basin
The Upper Penitencia Creek watershed is located in the southeastern Santa Clara Basin near the
northern end of the South Coast Ranges, a series of rugged subparallel mountain ranges that
extend 200 miles (322 kilometers) southeast from San Francisco (SCBWMI 2003). The Santa
Clara Basin is a northwest trending topographic depression that has largely evolved over the past
two million years as a result of tectonic uplift and erosion associated with three major branches of
the San Andreas Fault system: the San Andreas fault in the Santa Cruz Mountains to the west and
the Hayward and Calaveras faults in the Diablo Range to the east (Map 3). Only the San Andreas
and Calaveras faults are known to be active in the Santa Clara Basin, although the Hayward fault
is regarded as potentially active and is known to be active to the north. Many smaller faults are
also associated with each of these three main branches. Historical earthquake data indicate that
four to six moderate earthquakes have occurred in the Basin every decade since 1900 (Williams
1975).
Based on the review of available geologic information, topography within the Santa Clara Basin
is a result of years of faulting and uplift followed by erosion and deposition of gravel, sand, silt,
and clay from the Santa Cruz Mountains and Diablo Range (SCBWMI 2001). The elevations of
the surrounding peaks range from over 4,000 feet (1,200 meters) to below sea level, due to
subsidence, near Alviso at the southern end of San Francisco Bay. .
Principal geologic formations in the Santa Clara Basin are: the older, harder rocks of the
Franciscan Complex; the sedimentary units of the Santa Clara Formation and Cretaceous
sedimentary formation (Great Valley Sequence); and the unconsolidated materials of the valley
fill (SCBWMI 2003). The Franciscan Formation includes some rock originating from the basaltic
sea floor, but primarily consists of sedimentary rocks. Greenstone, blueschist, eclogite, chert,
shale, limestone, and serpentine are several of the rock types of the Franciscan Formation,
outcrops of which can be found within the Santa Cruz Mountains and Diablo Range.
The valley floor was originally below sea level and older sandstone units contain marine fossils.
The paleo-valley rose above sea level as sediments accumulated from sources in the surrounding
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mountains and once active volcanoes. During the Pleistocene (two million to 10,000 years ago),
the valley filled with gravel, sand, and silt eroded from the mountains, forming the Santa Clara
Formation. Outcrops of this formation are found along the valley margins and under the modern
valley floor. In the mid-to-late Pleistocene and early Holocene (one million to 8,000 years ago),
large volumes of sediment were transported from the mountains during a comparatively wet
climatic period. These deposits are often collectively referred to as older alluvium deposits. These
high-yield streams created alluvial fans with intervening valleys within the Santa Clara Basin.
Over the most recent 10,000 years, additional gravel, sand, silt, and clay has been transported
from the mountains and deposited within the valleys of the Basin. In some locations, these
deposits, typically referred to as the younger alluvium deposits, are over 1,500 feet (457 meters)
thick and are important sources of the groundwater in the Basin..
2.4.2
The descriptions and extent of the geologic formations and units within the Upper Penitencia
Creek basin are described in Table 2-2 and shown in Map 3. The basin lies within the Coast
Ranges physiographic province, a series of northwest trending coastal mountains, and drains the
Diablo Range, one of these coastal mountain ranges. The Diablo Range faces another set of
coastal mountains, the Santa Cruz Mountains, also in the South Coast Ranges, on the opposite
side of the valley that forms the Santa Clara Basin (SCBWMI 2003). The Upper Penitencia Creek
basin is comprised of four major geologic units interspersed between the Hayward and Calaveras
strike-slip fault zones. The fault zones run approximately parallel to one another in a north-south
direction, with the Calaveras fault running across the ridgetops at the basin divide. The basin is
underlain by the Franciscan formation, which is exposed on the eastern side of the Calaveras
fault. The Franciscan formation is a complex of sedimentary, sandstone and shale rocks, sheared
and deformed with pockets of chert, shale, and limestone interspersed with basalt lava flows
(BRG 2001, PWA 2003). After the Coast Ranges formed, the Upper Penitencia Creek Basin west
of the Hayward fault was flooded by seawater, burying the Franciscan rocks under layers of mud
and sand. These Tertiary and Quaternary sandstones, shales, and conglomerates are fragile and
easily erodible, forming well-rounded slopes that are dotted with landslides (BRG 2001). All the
units are deformed by strong seismic activity occurring between the two fault systems (BRG
2001). The urbanized and relatively flat Santa Clara Valley makes up roughly 12% of the
watershed area below Alum Rock Park, and is underlain by mostly unnamed Quaternary alluvial
fan and valley fill deposits (younger and older alluvium deposits).
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Table 2-2. Geologic units in the Upper Penitencia Creek Basin.
Acres
mi2
km2
Total
(%)
sand, gravel, silt, and mud
927
1.4
3.7
6.1
Mesozoic unnamed units
Serpentinite
50
0.1
0.2
0.3
Mesozoic Alum Rock Rhyolite
felsic volcanic rocks
73
0.1
0.3
0.5
5,272
8.2
21.3
34.9
4,022
6.3
16.3
26.6
167
0.3
0.7
1.1
404
0.6
1.6
2.7
963
1.5
3.9
6.4
310
0.5
1.3
2.1
66
0.1
0.3
0.4
159
0.2
0.6
1.0
178
0.3
0.7
1.2
2,065
3.2
8.4
13.7
422
0.7
1.7
2.8
36
0.1
0.1
0.2
23.6
61.2
100
Geologic Formation
Lithology
Holocene unnamed units
sheared sandstone and shale
(mélange)
low-grade metasandstone
Mesozoic Franciscan Complex
and shale
low-grade metavolcanic
rocks
porcellaneous or siliceous
mudstone and shale; chert
mudstone and shale, some
Mesozoic Great Valley Sequence
sandstone
sandstone and conglomerate,
Mesozoic Great Valley Sequence
some mudstone or shale
Pleistocene unnamed units
sand, gravel, silt, and mud
Quaternary undivided unnamed
units
Pliocene and/or Quaternary
unnamed units
low-grade metasandstone
and shale
mudstone and shale, some
sandstone
sandstone and conglomerate,
Upper Tertiary Briones Sandstone
some mudstone or shale
porcellaneous or siliceous
Upper Tertiary Monterey Group
mudstone and shale; chert
Open Water
N/A
WATERSHED TOTAL 15113
Source: SCVWD (GIS data)
1
Values reflect the areas calculated from the source data, and may differ from others in this report.
2.4.3
Landslides
Geologic mapping indicates active hillslope processes occurring within the Upper Penitencia
Creek Basin (BRG 2001). Landslides occur mostly in the steep-walled canyons of the upper basin
and include rockfall activity, shallow surface failures, and large, deep seated landslides that can
reactivate during large storms. Rockfall can occur from natural and anthropogenically controlled
mechanisms, through hillslope and bank-toe landslips, and road related failures caused by oversteepened slopes (PWA 2003). Landslides are most common on the Mesozoic Great Valley
sequence, a complex of conglomerate, sandstone, and shale, but are also found in areas underlain
by the Tertiary Briones or Monterey formations. Slope aspect appears to be an important factor in
hillslope stability with most failures occurring on the south facing slopes. A more detailed
quantitative analysis of landslide frequency within the basin was not possible with the available
data. Fine and coarse sediment can also be produced by gully erosion through tributary
rejuvenation, flow concentration from grazing, and flow concentration from road network
drainage (PWA 2003).
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2.5
2.5.1
Geomorphic Setting
Overview
Upper Penitencia Creek originates along Poverty Ridge within the Los Buellis hills on the
westernmost slopes of the Diablo Range, and flows into Coyote Creek before emptying into
southern San Francisco Bay (EOA 2003). The upper reaches are controlled by Cherry Flat
reservoir, but downstream the creek flows for one mile (1.6 kilometers) through a narrow, steep
walled canyon that has occasional exposed bedrock outcrops on either bank before reaching the
confluence with Arroyo Aguague, the largest tributary to Upper Penitencia Creek. Arroyo
Aguague originates along gently sloping ridgetops before flowing through a narrow canyon with
characteristics similar to the canyon below Cherry Flat reservoir. The two streams meet to form
the mainstem of Upper Penitencia Creek. Over the next 2.5 miles (4 kilometers), the mainstem
flows through Alum Rock Park, where it is artificially confined by rock walls built early in the
park’s history. Downstream of the park, Upper Penitencia Creek leaves its canyon and flows out
onto the floor of the Santa Clara Valley. In this highly urbanized section the channel has been
generally straightened and is confined by flood defense measures. Despite channel modifications,
the riparian habitat of Upper Penitencia Creek remains largely intact, and is one of the few
riparian corridors that contiguously stretches from the Diablo Range to Coyote Creek (SCBWMI
2003). The creek has flooded several times over the past century, and the channel is maintained to
ensure conveyance of these larger flood events (HDR 2002, EOA 2003). Existing flood control
structures along Upper Penitencia Creek are believed to provide adequate protection only against
smaller floods with a recurrence interval of less than about 10 years (J. Abel, SCVWD, pers.
comm., 2006).
Over the 11 miles (17.2 kilometers) from its headwaters to Coyote Creek, Upper Penitencia Creek
exhibits a single-thread planform, evolving from cascade and step-pool morphology in the
reaches below Cherry flat reservoir through Alum Rock Park to predominantly pool-riffle with
occasional plane-bedding downstream across the valley floor to Coyote Creek. Median (D50) bed
grain size generally decreases from headwater to mouth, although there are many locations within
the urbanized valley where large, unnatural clasts (concrete, bricks, rubble) have been added to
the stream to support the banks and prevent unwanted erosion (PWA 2003, Jordan et al. 2005).
Signs of channel incision are apparent downstream of the confluence of Upper Penitencia Creek
and Arroyo Aguague. Through Alum Rock Park there are occasional lengths where the channel
has been scoured to bedrock, and downstream on the valley floor the bed appears to generally
aggrade as it flows toward Coyote Creek, with the exception of a highly incised section near the
mouth. Some incised sections were observed between the downstream edge of the park and
Coyote Creek, but these may represent the natural behavior of an alluvial channel as it meanders
across its valley and responds to episodic sediment delivery from upstream reaches.
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2.5.2
General Description
The potential historical geomorphic condition of the Upper Penitencia Creek Basin was
determined by examining the processes of sediment input and transport occurring throughout the
channel network. River channels show distinct bed morphologies in response to their capacity to
transport sediment and the supply of available sediment (Montgomery and Buffington 1997). In a
natural setting, the ability of a channel to transport sediment is largely influenced by gradient and
the supply is governed by delivery sources and mechanisms. An understanding of natural
sediment dynamics and channel response is essential to understand and describe the current
condition of impaired channels. The historical geomorphic condition was assumed to be the
potential condition of the basin before European influence.
Upper Penitencia Creek below Cherry Flat reservoir, and the adjacent Arroyo Aguague sub-basin,
flow through a tightly confined, steep walled, bedrock controlled valley. Under historical
conditions the dominant sediment sources would include landslides, which were likely prevalent
due to the basin’s tectonic activity, and erosion of the weak parent material. Sediment delivery to
the stream channel was facilitated by the episodic rainfall characteristic of the area’s
Mediterranean climate and influenced by the orographic effects of storm clouds being forced over
the Diablo Range. The relatively steep gradient (4–10%) and narrow valley would result in a
channel where the sediment transport capacity exceeded the sediment supply, leaving bedrock
cascades, and large clasts that form a step-pool morphology (Montgomery and Buffington 1997,
EOA 2003). Fine sediment would either be largely absent, in the case of cascade reaches, stored
in step-pools, along the channel margins, or near boulders and large woody debris (LWD). The
reach would be a sediment transport zone that delivers sediment to lower gradient reaches
downstream. The narrow valley and the high sediment transport capacity would leave few
extensive gravel bars or floodplain surfaces for riparian recruitment, but the valley walls and
upslope areas likely supported an extensive riparian canopy. The influence of LWD on channel
form would likely be limited as logs quickly break down from abrasion against boulders and
pieces lie above the channel, resting on boulders.
Downstream of its confluence with Arroyo Aguague, the mainstem of Upper Penitencia Creek
flows through a moderately confined alluvial valley. The dominant sediment sources are, and
likely were, fluvial transport, landslides, and debris flows. Naturally occurring summer wildfires
followed by winter rains likely caused debris flows that periodically aggraded the channel,
causing the creek to meander across its valley (BRG 2001). The average gradient is 3% and such
reaches are typically dominated by step-pool and plane-bed morphologies. Plane-bedding occurs
in relatively steep gradients where rivers are unable to form pools and riffles because of low
width to depth ratios and coarse bed substrates that diminish lateral flow (Montgomery and
Buffington 1997). Pool-riffle bed morphologies are able to form in plane-bedded environments in
the presence of flow obstructions, such as large woody debris (LWD) (Montgomery et al. 1995).
In a natural setting, the channel would meander across the narrow valley, laterally influenced by
landslides that redirect the channel, and create gravel bars and floodplains that would be the site
of riparian regeneration and recruitment. The availability of geomorphic surfaces would create a
riparian forest that contributes LWD to the stream channel and encourage the formation of a
forced pool-riffle morphology.
Downstream of Alum Rock Park, Upper Penitencia Creek leaves its confined canyon and flows
out onto a low, unconfined alluvial plain. The main sources of sediment here were likely from
fluvial transport and bank erosion, as is generally the case today. The average gradient is less than
1% and would most likely support plane-bedded and pool riffle channel morphologies. The
presence of pool-riffle channels is influenced by the grain size, with smaller sizes favoring the
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11
formation of pool-riffle sections, and by the presence of LWD, which would be a main
component of pool formation. Reaches with higher volumes of woody debris tend to have shorter
distances between pools, and a greater pool frequency (Abbe and Montgomery 1996).
In a natural state, sediment from headwater sections would be supplied to downstream alluvial
sections to be reworked by periodic floods, resulting in a temporal mosaic of depositional patterns
and sites (PWA 2003). Flow would be confined to semi-permanent alluvial channels that
gradually filled with sediment, causing overtopping and channel switching. Unimpaired flows
during the winter and spring rainy season would have overtopped banks and inundated vegetated
banks and floodplains, providing organic matter to support the stream food web, dissipating
stream power, and serving as important seasonal feeding, rearing, and low-velocity overwintering
habitat for juvenile salmonids. Gravel was likely present as localized deposits (e.g. gravel bars)
and intermixed with some fine sediment due to the erosive nature of the parent material, but still
able to provide good spawning habitat and macroinvertebrate production.
2.5.3
Disturbance Factors
The primary anthropogenic activities influencing the sediment dynamics and the current
geomorphic condition of the Upper Penitencia basin are water diversion, roads, channel
modification, urbanization, and cattle grazing. Cherry Flat dam was originally a water source for
Alum Rock Park and several local ranchers, as well as a flood control structure (EOA 2003). The
park no longer uses the reservoir as a water source, but the city still manages the facility for flood
control and to maintain a wetted channel downstream (BRG 2001) (see Section 2.2).
Land use in the portion of the basin upstream of the confluence of Upper Penitencia Creek and
Arroyo Aguague includes grazing, scattered residential development, parkland, and undeveloped
forest (SCBWMI 2001). Grazing occurs on private lands upstream of Alum Rock Park in the
Upper Penitencia Creek (Buchan et al. 1999, EOA 2003) and Arroyo Aguague drainages
(SCBWMI 2003). The intensity of the grazing is unknown, as most of the grazed areas are
privately owned with few access roads. Grazing pressure in the upper basin can create several
potential impacts, including soil compaction, loss of vegetative cover, alteration of plant species
composition, and destabilization of hillslopes and stream banks (Mount 1995). Soil compaction
reduces infiltration capacity and increases runoff to speed gully formation. The loss of vegetative
cover reduces rainfall interception to further increase runoff and erosion, and may increase stream
temperatures through lack of canopy cover. Removal of native grassland species intensifies the
increases in runoff and erosion, as natives bind soils more cohesively than exotic annual grasses.
Along the stream corridor, livestock can feed on riparian seedlings, preventing regeneration and
destabilizing banks. In some cases, such as below Cherry Flat Reservoir, cattle are allowed access
to the channel (EOA 2003).
The road network in the basin upstream of the confluence of Upper Penitencia Creek and Arroyo
Aguague is limited to a few public and private roads. However, the majority of the roads are
native surfaced (dirt), and it is possible that they contribute some sediment to the Upper
Penitencia Creek channel. Road-related surface erosion can be a large source of the fine sediment
that enters streams (Reid and Dunne 1984), and much of this sediment originates at or near
locations where roads cross or divert streams (Furniss et al. 1991). Road surfaces collect water
and concentrate flow directly into stream channels or over hillslopes (Forman and Alexander
1998). Flow concentration over steep hillslopes initiates gully formation and lengthens the first
order drainage network, which can lead to increases in erosion (Montgomery 1994). Landsliding
and mass wasting associated with roads can be a major source of fine sediment to the channel and
exposed cut/fill sites along roadways are also likely sources of fine and coarse sediment (Forman
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12
and Alexander 1998). The amount of sediment produced from roads in the Upper Penitencia
Creek watershed, and potential for delivery to the channel network, has not been documented.
The lower four miles (6.4 kilometers) of the basin are influenced by a variety of flood control
structures and activities: bank reinforcement, channel straightening, and bypass channels. The
creek has flooded several times over the past century and the streams are maintained to prevent
flooding through sediment removal, vegetation management, and bank protection. As discussed
in Section 2.5.1, existing flood control structures along the creek appear to provide adequate
protection against smaller floods (< 10 year recurrence interval) (J. Abel, SCVWD, pers. comm.,
2006).
2.5.4
Current Condition by Study Reach
There have been several previous reach classifications developed for Upper Penitencia Creek
(Table 2-3). All of the previous classifications acknowledge a morphological and land-use change
at the downstream end of Alum Rock Park, where Upper Penitencia Creek flows out of its canyon
and onto its alluvial fan, and where it leaves a lightly urbanized portion of the basin and enters the
highly urbanized Santa Clara Valley. Upstream and downstream of this point, the previous reach
designations vary according to the goals of the particular study and the criteria used to develop
the classification. The reaches developed here were based on geomorphic processes, and thus
vary slightly from those previously reported.
Table 2-3. Reaches of Upper Penitencia Creek developed for this report and derived from other
sources.
River
Mile
SWS
(2005)
0.00
0.25
0.50
0.75
1.00
1.25
1.50
1.75
2.00
2.25
2.50
URB 5
Mouth to King
Rd
URB 4
King Road to
Mabury Rd
URB 3
Mabury Rd to
Capitol Ave
2.75
3.00
3.25
3.50
3.75
4.00
4.25
4.50
4.75
5.00
5.25
5.50
5.75
6.00
URB 2
Capitol Ave to
Piedmont Ave
SCBWMI
(2003)
Reach 1
Mouth to N.
Jackson Ave
Reach 2
N. Jackson Ave
to Alum Rock
Park Entrance
URB 1
Piedmont Ave to
Dorel Drive
ARP 3
Dorel Drive to
Quail Hollow
crossing
Reach 3
Alum Rock Park
Entrance to
Arroyo Aguague
mouth
FAHCE
Database (2000)
PWA
(2003)
SCVURPPP
(2003)
Reach 1
Mouth to
Capitol Ave
Reach 5
Mouth to King
Bridge Rd
Reach 4
King Road to
Mabury Road
Reach 3
Mabury Rd
to Capitol Ave
Reach 1
Mouth to King
Bridge Rd
Reach 2
King Road to
Mabury Road
Reach 3
Mabury Rd
to Capitol Ave
Reach 2
Capitol Ave to
Nobel Ave
Reach 3
Nobel Ave to
Arroyo
Aguague mouth
Reach 2
Capitol Ave to
Piedmont Ave
Reach 1
Piedmont Ave
to Tallent Rd
NOT
OBSERVED
Reach 4
Capitol Ave to
Dorel Dr
Reach 5
Dorel Dr to
Arroyo Aguague
mouth
ARP 2
Quail Hollow
crossing to most
upstream drop
structure
ARP 1
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River
Mile
SWS
(2005)
6.25
6.50
6.75
7.00
7.25
7.50
7.75
8.00
8.25
8.50
8.75
9.00
Drop structure to
confluence
UUP
Arroyo Aguague
mouth to Cherry
Flat Dam
SCBWMI
(2003)
FAHCE
Database (2000)
Reach 4
Arroyo Aguague
mouth to Cherry
Flat Dam
Reach 4
Arroyo
Aguague mouth
to tributary
downstream of
Cherry Flat Dam
PWA
(2003)
SCVURPPP
(2003)
Reach 6
Arroyo Aguague
mouth to Cherry
Flat Dam
NOT
OBSERVED
CHERRY FLAT DAM
Upper Penitencia Creek below Cherry Flat Reservoir to confluence with Arroyo Aguague
Upper Penitencia Creek below Cherry Flat reservoir (UUP, RM 8.1–6.7) is fed a steady supply of
coarse and fine sediment from landslides and rockfalls that scar the canyon sides. Other sources
of mass movement include sheetwash, and deep-seated landslides that dot the landscape and can
be reactivated during wet periods (PWA 2003). The bed is composed of angular and semi-angular
large cobbles to large boulders, with pockets of sandy clay along margins and behind channel
obstructions. The channel morphology is step-pool and cascade, but with varying step-lengths,
possibly due to the constant input of large boulders from the hillsides or the influence of tectonic
activity. Woody debris has a minimal effect on sediment storage and channel geometry due to the
presence of boulders that prevent the logs from interacting with the bed surface. Five hundred
meters upstream of its confluence with Arroyo Aguague, Upper Penitencia Creek flows through a
narrow channel constriction at a sharp bend in the channel that impounds mobile bed material and
small and large boulders. Accumulations of sandy clay up to 18–24 inches [46–61 centimeters]
thick are locally stored upstream and downstream of boulders, which can be characteristic of
cascade channels where gravel and finer material is stored in the stoss and lee sides of flow
obstructions due to physical impoundment and generation of velocity shadows (Montgomery and
Buffington 1997). Downstream of the bend, the creek flows over a 20 to 30 foot cascading
waterfall into a small bedrock pool. Down to the confluence with Arroyo Aguague, the channel is
slightly wider, with a lower gradient and slightly smaller bed material, ranging from medium
cobbles to small boulders. Pockets of clay persist along the channel margins, but the bed sediment
generally appears better mixed with gravel and sand. In their assessment of the FAHCE (2000)
database, EOA (2003) noted high levels of fine substrate and embeddedness of gravel substrates
in this reach.
Arroyo Aguague
The upper reaches of the Arroyo Aguague (AAG, [RM not assigned]) sub-basin occur within the
Calaveras fault zone over highly erodible and fractured Mesozoic era geologic units. From these
upper reaches, Arroyo Aguague flows through a narrow canyon, with steep walls that are rife
with small landslides and earthflows that provide a consistent source of fine and coarse sediment.
Also present are less frequent, but large scale, Quaternary landslides (BRG 2001). These reaches
are characterized by rounded to semi-rounded boulders forming a step-pool to cascade stream
morphology. Pockets of gravelly sand are stored upstream and downstream of large boulders
within and along the channel margins. The influence of woody debris on sediment storage is also
minimal in this reach due the perching of logs above the bed surface, and rapid decomposition
and abrasion of recruited hardwood logs. Still, occasional fallen trees that span the channel and
remain attached at the rootwad to the opposite bank are able to form small debris jams that trap
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14
mobile sediment and exert some control on bed elevation. Such pockets of mobile sediment may
be indicative of the sizes of sediment delivered to downstream reaches.
Pockets of fine sediment were observed in this portion of Upper Penitencia Creek and in Arroyo
Aguague during reconnaissance surveys, but it was not possible to determine if these were
attributable to a naturally high sediment yield due to erosive parent material, tectonic activity, and
episodic rainfall, or represent an elevated supply in response to adjacent land uses, such as
grazing and roads.
Upper Penitencia Creek through Alum Rock Park
Upper Penitencia Creek through Alum Rock Park was divided into three reaches based on the
differences in bed morphology observed during a geomorphic reconnaissance, the degree of
confinement, and the intensity of surrounding land uses related to the park (Table 2-3).
The first reach (ARP 1, RM 6.7–6.1) begins at the confluence of Upper Penitencia Creek and
Arroyo Aguague and extends downstream to the first in a series of grade control structures. The
reach is characterized by a 3–4 meter wide unpaved trail along the right bank, and rock walls and
bank revetments running along portions of the channel. There is also a paved road along the steep
valley wall about 200 m upslope of the right bank. The creek is moderately to tightly confined to
its active channel by rock walls and bank revetments intended to prevent local bank erosion and
to protect the adjacent trail. BRG (2001) mapped several landslides along both banks. The level
of channel confinement gradually increases downstream, as does the depth of incision. The
resulting channel is composed of step-pool and plane bed morphologies with few pieces of LWD
in the channel.
The next reach (ARP 2, RM 6.1–5.1) begins downstream of the first grade control structure and
extends downstream into the heart of Alum Rock Park. The reach is narrowly confined along both
banks by rock walls and riprap, and park infrastructure (buildings, trails, several parking lots)
occupies adjacent terraces on both banks. The creek is limited to its active channel, with little or
no room for channel migration. Sediment delivery from hillslopes and banks is reduced and since
the channel is unable to erode its banks or meander, the channel is generally cutting downward
(BRG 2001). Attempts to control this incision with grade control structures have created
alternating stretches of empty channel scoured to bedrock (cascades), step-pool, and plane bedded
morphologies. As the channel is confined to a narrow path and prevented from meandering, there
is a lack of new floodplains for riparian forest regeneration and a lack of LWD recruitment.
The downstream reach (ARP 3, RM 5.1–3.9) extends downstream from the covered bridge to the
road crossing at Dorel Drive, which is where Upper Penitencia Creek flows out onto its alluvial
fan. The reach is moderately controlled on the banks by cement walls and riprap, and has a road
and paved trails running along the adjacent terraces. There is some resumption of sediment
delivery from the banks and hillslopes, with the creek eroding its banks and undermining some
bank revetment structures at the top of the reach, and a large active landslide near the downstream
end.
Upper Penitencia Creek downstream of Alum Rock Park
The reaches downstream of the canyon mouth are generally depositional in nature due to their
distance below the main sediment sources of the basin. The deposition gradually increases in the
downstream direction as overall channel slope lessens, until the final 0.7 miles (1.1 kilometers)
when the channel incises rapidly before emptying into Coyote Creek. Upper Penitencia Creek
along the Santa Clara Valley floor was divided into five reaches based on differences in bed
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morphology, channel confinement, and intensity of surrounding land uses observed during
geomorphic reconnaissance and from available literature.
The most upstream urban reach (URB 1, RM 3.9 to 3.1) is a natural channel with few structural
modifications, limited to bank revetments around bridges and near roads (EOA 2003). There are
some incised sections occurring near adjacent roadways and several meandering sections with
well developed gravel bars. Overall the reach displays a meandering channel form with gravel
bars and an active floodplain surrounded by a relatively wide riparian corridor. PWA (2003)
noted no apparent systematic evidence of channel erosion/incision, but did observe channel
deepening at the downstream end of the reach. Portions of this reach appear to have been
straightened near the downstream end (J. Abel, SCVWD, pers. comm., 2006).
The next downstream reach (URB 2, RM 3.1–2.2) has incised sections occurring near roadways
and meandering sections with gravel bars surrounded by a generally wide riparian corridor. The
reach is a zone of greater sediment production due to intermittent bank erosion that is likely
caused by the constraining effects of high flows on the banks, knick point migration, and
sediment deposition diverting flow toward banks (PWA 2003). Finer material on the bed could
indicate a depositional environment. PWA (2003) described this reach as a zone of aggradation,
with a sediment imbalance of +1,865 tonnes/year (1,865,000 kilograms/year). This value was not
corroborated in the field, and is not a true measure of annual sediment yield, but does indicate the
relative ability to transport sediment between reaches.
Reach URB 3 (RM 2.2–1.4) is an incised channel with few bedforms, modified by an earthen
levee (EOA 2003, PWA 2003). The reach grades progressively downward from the top of the
reach, with at least one knickpoint and channel avulsion, indicating some channel instability. At
the downstream end of the reach, PWA (2003) observed a channel avulsion possibly associated
with downstream disturbance and knickpoint migration. PWA (2003) also considered this reach
to be a zone of net sediment deposition (+1,982 tonnes/year [1,982,000 kilograms/year]), with
most deposition concentrated between Interstate 680 and Jackson Avenue.
Reach URB 4 (RM 1.4–0.7) is a moderately incised channel with limited floodplain access and is
lined by an earthen levee (EOA 2003). This portion of Upper Penitencia Creek is straight with
moderate connection to the floodplain (PWA 2003). There are numerous signs of current and past
bank erosion, which is partially controlled by bank revetments, but potentially exacerbated by
channel edge embankments. Some bank erosion may have been arrested by the construction of
the flood spillway at the downstream end of the reach. Downstream of flood bypass there are
some signs of contemporary bank erosion focused outside of bends. PWA (2003) described this
as a zone of sediment deposition, with input exceeding export by 15 tonnes/year (15,000
kilograms/year).
The most downstream reach (URB 5, RM 0.7–0.0) flows into Coyote Creek and is the most
incised of all the reaches in the urbanized portion of the basin. This reach was created between
1873 and 1875 when Upper Penitencia Creek was diverted into Coyote Creek, and is therefore
most of it is an artificially straight section. The section between King Road and Berryessa Road is
incised but likely follows the natural stream course (J. Abel, SCVWD, pers. comm., 2006). The
banks are heavily protected with little indication of bank erosion and no floodplain connectivity.
PWA (2003) found this to be a reach of net sediment transport (-660 tonnes/year [660,000
kilograms/year]). A sand bar sometimes forms at the confluence with Coyote Creek (PWA 2003;
J. Abel, SCVWD, pers. comm., 2005).
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The highest level of natural floodplain and channel function are observed in UUP, AAG, ARP 1
and URB 1, where channel modifications are either absent or have minor influence on sediment
dynamics. The reaches upstream of Alum Rock Park (UUP and AAG) are relatively unaffected
by urbanization, but are influenced by surrounding land uses. In the upper Alum Rock Park reach
(ARP 1) the creek flows through a relatively wide, well vegetated inset valley without numerous
man-made impediments, such as concrete weirs or bridge footings. In the upper urban reaches
(URB 1 and 2) the creek flows across an alluvially deposited surface with vegetation on both
banks. The lack of confinement allows point and lateral bars to develop naturally in these reaches,
adding roughness to the channel and creating greater curvature, or sinuosity. In this way, the
equilibrium between available transport capacity and sediment supply within the reach is better
maintained. In the two lower Alum Rock Park reaches (ARP 2 and 3), and the lower urban
reaches (URB 3, 4, and 5), channel and floodplain function progressively degrade as the channel
narrows and modifications encroach on the creek. Here, the channel is straight, point and lateral
bars shrink or disappear altogether, and an increasing number of concrete walls and weirs act as
grade control and bank stabilizing structures. Transport capacity increases as the number of
roughness elements (i.e., bedforms, bar deposits, sinuosity) decrease and anthropogenic
influences increase. As a result, a greater amount of scour and incision was observed in these
reaches.
It was not possible for this study to quantitatively assess the effects of land use changes along
Upper Penitencia Creek. Literature review and field observations indicate, however, that despite
little change in channel planform through the 20th century (Figure 2-3), the channel profile may
still be adjusting to the recent decades of urbanization in the basin as shown by evidence of
incision, and multiple occurrences of channel avulsion and knickpoint migration. These changes
likely have impacted the physical processes that govern sediment movement and channel stability
in Upper Penitencia Creek, and likely have altered the structure and function of aquatic habitat.
Changes in physical habitat are discussed further in Section 4.2.
2.6
Fish Community Composition
Eight native fish species have been documented in the Upper Penitencia Creek watershed,
including federally listed steelhead (Oncorhynchus mykiss) and its resident form rainbow trout, as
well as Pacific lamprey (Lampetra tridentata), California roach (Lavinia symmetricus), hitch
(Lavinia exilicauda), Sacramento blackfish (Orthodon microlepidotus ), Sacramento sucker
(Catostomus occidentalis), prickly sculpin (Cottus asper) and riffle sculpin (Cottus gulosus)
(Buchan et al. 1999, Leidy 1984). Each of these species has been documented upstream to Dorel
Drive, near the entrance to Alum Rock Park, and five of these species have been observed farther
upstream. Sacramento blackfish documented in Upper Penitencia Creek may have been
temporary introductions via water imports from the South Bay Aqueduct (J. Abel, SCVWD, pers.
comm., 2006). Pacific lamprey and Sacramento sucker have occasionally been observed within
Alum Rock Park, while steelhead/resident rainbow trout, California roach, and riffle sculpin have
been observed up to the waterfall fish barriers in both Upper Penitencia Creek and Arroyo
Aguague (Buchan et al. 1999). During snorkel surveys conducted in May 2005 by Stillwater
Sciences, we observed three native species (or genera) in Upper Penitencia Creek within Alum
Rock Park: Oncorhynchus mykiss, Lavinia sp., and Cottus sp. California roach and rainbow trout
are the only two native species that have been observed upstream of the waterfall fish barrier in
Upper Penitencia Creek, whereas only resident rainbow trout have been observed upstream of the
waterfall fish barrier in Arroyo Aguague (Buchan et al. 1999). Chinook and coho salmon may
have historically occurred in Upper Penitencia Creek (Buchan et al. 1999, Leidy et al. 2005), but
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insufficient evidence exists to confirm this. Chinook salmon have at times spawned in the lower
reaches of Upper Penitencia Creek, which apparently contains better spawning and rearing habitat
than the Coyote Creek mainstem (Smith 1998, FAHCE 2003).
Information on historical fish species composition and distribution in Upper Penitencia Creek is
limited. However, it is generally thought that Upper Penitencia Creek is the main producer of
steelhead for the Coyote Creek basin (Li, unpublished data). Upper Penitencia Creek is one of
only a few creeks in the South Bay that support steelhead runs (Buchan et al. 1999) and is
considered to have the best steelhead habitat (SCBWMI 2003).
Introduced fish, including inland silverside (Menidia beryllina), goldfish (Carassius auratus),
fathead minnow (Pimephales promelas), mosquitofish (Gambusia affinis), bluegill (Lepomis
macrochirus), green sunfish (Lepomis cyanellus), largemouth bass (Micropterus salmoides), and
white catfish (Ictalurus catus) have been observed in the lower reaches of Upper Penitencia
Creek, with some observed as far upstream as Dorel Drive, near the entrance of Alum Rock Park
(SCVURPPP 2003a; Li, unpubl. data). Green sunfish and goldfish have been identified further
upstream within Alum Rock Park (BRG 2001, Buchan et al. 1999). Bluegill is the only nonnative species observed between the waterfall fish barrier and Cherry Flat Dam, most likely due
to releases from Cherry Flat Reservoir (Buchan et al. 1999). During snorkel surveys conducted by
Stillwater Sciences in May 2005, bluegill were also observed in Upper Penitencia Creek just
downstream of the Arroyo Aguague confluence and in Arroyo Aguague downstream of the
waterfall.
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3
ANALYSIS SPECIES
One of the premises of the limiting factors analysis for the Upper Penitencia Creek watershed was
that a select “analysis species" could be used for evaluating the impacts of watershed activities on
a range of aquatic species historically and currently found within the basin. An analysis focused
on the life history and habitat requirements of a certain species allows us to improve our
understanding of the relative importance of various watershed processes and habitat features,
identify factors currently limiting the distribution and abundance of the species in the watershed,
and evaluate the degree to which watershed-level management strategies may benefit the species,
as well as other species and the ecosystem as a whole. Additionally, an assessment of the factors
that may be limiting the success of the analysis species at each freshwater life stage helps
evaluate the impact of a specific stressor (e.g., sediment) at multiple temporal and spatial scales.
Steelhead was chosen by SCVURPPP as the analysis species for the Upper Penitencia Creek
Limiting Factors Analysis because this species: (1) has special-status designation, (2) has high
economic or public interest value, (3) has narrow habitat requirements, (4) is dependent on
habitats that have likely been reduced in quality and quantity from historical conditions because
of anthropogenic land use within the basin and elsewhere, (5) is in decline locally and regionally,
and (6) has habitat requirements that represent the needs of a suite of native coldwater fish
species. Steelhead, and its resident form rainbow trout, are the only salmonids currently present in
Upper Penitencia Creek (Leidy et al. 2003). Steelhead occupy perennial stream habitat within the
Upper Penitencia Creek watershed upstream to barrier waterfalls in Upper Penitencia Creek and
Arroyo Aguague (Figure 3-1), its largest tributary.
Restoring or maintaining habitat connectivity and habitat-forming processes targeted at steelhead
will likely benefit other native coldwater species found in the watershed. Their potential
sensitivity to land use practices within the watershed, as well as their limited distribution,
represents a clear example of a species in decline for which habitat conservation is an important
consideration.
3.1
Steelhead Status and Life History Overview
Steelhead found in the Upper Penitencia Creek watershed belong to the Central California Coast
evolutionarily significant unit (ESU) (NMFS 1997), which includes coastal drainages from the
Russian River to Aptos Creek and the drainages of San Francisco and San Pablo Bays, excluding
the Sacramento-San Joaquin River basin. This ESU is federally listed as threatened under the
Endangered Species Act (NMFS 2000).
Accurate adult population size estimates for Upper Penitencia Creek and other South San
Francisco Bay watersheds are not available (Leidy et al. 2003; J. Smith, San Jose State
University, pers. comm., 2004). In general, steelhead stocks throughout California have declined
substantially. The most current estimate of the population of steelhead in California is
approximately 250,000 adults, which is roughly half the adult population that existed in the mid1960’s (McEwan and Jackson 1996). Currently, 10 or fewer tributaries to San Francisco Bay are
estimated to support runs of steelhead, with most streams having runs of 50 or fewer spawning
adults (Leidy et al. 2003). A summary of the life history and habitat requirements of steelhead is
provided below and the general steelhead life cycle is presented in Figure 3-2. Detailed
information regarding this species is provided in Appendix B.
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Steelhead is the term commonly used for the anadromous life history form of rainbow trout. In
Upper Penitencia Creek, both resident and anadromous life histories are thought to be displayed
(Smith 1998), although detailed information on the relative proportion of each ecotype is not
available. For convenience, we use the term steelhead throughout this report to describe all O.
mykiss in the Upper Penitencia Creek watershed. The relationship between anadromous and
resident life history forms of this species is the subject of ongoing research. Current evidence
suggests that the two forms are capable of interbreeding and that, under some conditions, either
life history form can produce offspring that exhibit the alternate form (i.e., resident rainbow trout
can produce anadromous progeny and vice-versa) (Shapovalov and Taft 1954, Burgner et al.
1992, Hallock 1989). The fact that little to no genetic differentiation has been found between
resident and anadromous life history forms inhabiting the same basin supports this hypothesis
(Busby et al. 1993, Nielsen 1994, but see Zimmerman and Reeves 2001).
Steelhead return to spawn in their natal stream, usually in their fourth or fifth year of life, with
males typically returning to freshwater earlier than females (Shapovalov and Taft 1954, Behnke
1992). A small percentage of steelhead may stray into streams other than their natal stream.
Based on variability in the timing of their life histories, steelhead are broadly categorized into
winter and summer reproductive ecotypes. Only the winter ecotype (winter-run) occurs in Upper
Penitencia Creek. Winter-run steelhead generally enter spawning streams from late-fall through
spring as sexually mature adults, and spawn in late winter or spring (Roelofs 1985, Meehan and
Bjornn 1991, Behnke 1992). Spawning occurs primarily from January through March, but may
begin as early as late December and may extend through April (Hallock et al. 1961).
Female steelhead construct redds in suitable gravels, often in pool tailouts and heads of riffles, or
in isolated patches in cobble-bedded streams. Steelhead eggs incubate in the redds for 3–14
weeks, depending on water temperatures (Shapovalov and Taft 1954, Barnhart 1991). After
hatching, alevins remain in the gravel for an additional 2–5 weeks while absorbing their yolk
sacs, and then emerge in spring or early summer (Barnhart 1991).
After emergence, steelhead fry move to shallow-water, low-velocity habitats, such as stream
margins and low-gradient riffles, and forage in open areas lacking instream cover (Hartman 1965,
Fontaine 1988). As fry grow and improve their swimming abilities in late summer and fall, they
increasingly use areas with cover and show a preference for higher velocity, deeper mid-channel
areas near the thalweg (the deepest part of the channel) (Hartman 1965, Everest and Chapman
1972, Fontaine 1988).
Juvenile steelhead (parr) rear in freshwater before outmigrating to the ocean as smolts. The
duration of time parr spend in freshwater appears to be related to growth rate, with larger, fastergrowing members of a cohort smolting earlier (Peven et al. 1994). Steelhead in warmer areas,
where feeding and growth are possible throughout the winter, may require a shorter period in
freshwater before smolting, while steelhead in colder, more northern, and inland streams may
require three or four years before smolting (Roelofs 1985).
Juvenile steelhead occupy a wide range of habitats, preferring deep pools as well as higher
velocity riffle and run habitats (Bisson et al. 1982, Bisson et al. 1988). During periods of low
temperatures and high flows that occur in winter months, steelhead prefer low-velocity pool
habitats with large rocky substrate or woody debris for cover (Hartman 1965, Raleigh et al. 1984,
Swales et al. 1986, Fontaine 1988). During high winter flows, juvenile steelhead seek refuge in
interstitial spaces in cobble and boulder substrates (Bustard and Narver 1975).
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Juvenile emigration typically occurs from March through June. Emigration appears to be more
closely associated with size than age, with 6–8 inches (15–20 centimeters) being most common
for downstream migrants. Depending partly on growing conditions in their rearing habitat,
steelhead may migrate downstream to estuaries as age 0+ juveniles or may rear in streams for up
to four years before outmigrating to the estuary and ocean (Shapovalov and Taft 1954). Steelhead
migrating downstream as juveniles may rear for one month to a year in the estuary before
entering the ocean (Shapovalov and Taft 1954, Barnhart 1991).
3.2
Steelhead Life History and Habitat Use Conceptual Model
In this section, we describe a conceptual model for linkages between physical habitat and the life
history of steelhead. We then briefly discuss how existing steelhead abundance data and results
from population surveys conducted during this study were used to screen the initial list of
potential limiting factors to develop a list of hypotheses specific to the Upper Penitencia Creek
watershed.
Generally speaking, a wide range of factors may limit the size and growth potential of a
population of organisms. While each of these factors may serve as the primary limiting factor
under specific circumstances, our goal was to identify the factor or factors that appeared to be
limiting the population of steelhead under current conditions in Upper Penitencia Creek. The
primary aim of this analysis was to use knowledge of various potential limiting factors combined
with information gathered from focused studies to examine the importance of sediment-related
impacts relative to other potential limiting factors. This knowledge will help elucidate the causeand-effect relationships between land use and water management activities in the watershed and
their effects on steelhead and general aquatic ecosystem health.
We first provide a general conceptual model that is used as the starting point for developing
conceptual models specific to Upper Penitencia Creek. The general model combines hypotheses
that are well supported by the literature with elements that are the subject of ongoing research,
but is not intended to be a detailed account of the life cycle and habitat requirements for steelhead
(such an account is provided with references in Appendix B). Rather, this formulation provides a
starting point for exploring available data and developing hypotheses. It is expected that there
will be cases where our general conceptual models do not hold up, requiring subsequent
modification to fit the conditions of particular watersheds.
3.3
Conceptual Model
Steelhead can smolt at a variety of ages, but most frequently smolt at ages 1+ and 2+1. Because
juvenile steelhead must spend at least one summer and winter in freshwater prior to outmigrating
to the sea, they tend to establish territories2 in suitable rearing habitat soon after emergence from
the gravel (as opposed to fall Chinook, chum, pink, and sockeye salmon, which only spend a few
days, weeks, or months within their natal stream). The maximum densities of oversummering age
0+ steelhead that a reach of stream can support are determined by territorial/agonistic behavior,
1
We follow conventional methods for assigning fish ages to year classes. Age 0+ refers to fish in their first year of life, sometimes
called young-of-the-year; age 1+ to fish in their second year of life, and so on. A fish changes from age 0+ to age 1+ based on the
time of hatching, which in the case of steelhead occurs in the spring.
2
We use the term territory and territory size not only in its traditional sense—as a particular defended area —but also in cases where
defense of a particular area may not occur but agonistic behavior by dominant individuals (e.g., nips, fin extensions, charges)
effectively determine the maximum density of rearing juvenile steelhead in an area.
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both intraspecific and interspecific with other salmonids when they are present. Aggressive
displays such as gill flaring, fin extensions, charges, and attacks are used to actively defend
individual territories. This behavior results in density-dependent emigration or mortality of
juvenile steelhead that do not successfully establish and defend territories.
The size of steelhead territories may vary from location to location or between seasons as a
function of food availability and temperature, becoming smaller when habitats are more
productive or when they are colder. Whether territories are relatively large or small, the forming
of territories during freshwater rearing provides an important mechanism for partitioning a finite
food resource among individuals and regulating the growth of juvenile steelhead. If territories
were not established and defended by individuals, the result would either be mortality of many
juveniles due to starvation or the production of a large number of small smolts that, as we discuss
below, would have very poor ocean survival.
Steelhead smolts tend to have much greater survival to adulthood if they outmigrate as age 2+ or
older smolts because the older fish are generally larger. Although they are sometimes common,
age 1+ smolts may contribute little to the numbers of returning adults3. This differential survival
is likely due to the advantages that larger fish have in evading predation, either through superior
swimming ability or by surpassing the gape size of potential predators. In considering steelhead
life histories, it is important to distinguish between age 1+ smolts and age 1+ downstream
migrants. It is a common life history strategy for juvenile steelhead to migrate downstream in the
spring but rear for an additional year before smolting in an estuary when one is present. This is
true of all age classes of juvenile steelhead but especially common at age 1+. Age 1+ steelhead
that rear in the estuary will then smolt at age 2+ the following spring and, because they may be
larger as a result of greater food supply in the estuary, they may experience similar if not higher
survival to adults as stream-reared age 2+ smolts. Therefore, both in instances of stream rearing
and estuary rearing, production of adult steelhead depends greatly on the size of the smolts
produced and advantageous smolt size is most often reached by age 2+.
The relatively extended freshwater rearing of steelhead has important consequences for its
population dynamics. The maximum number of steelhead that a stream can support is limited by
food and space through territorial behavior, and this territoriality is necessary to produce
steelhead smolts that are large enough to have a reasonable chance of ocean survival. Because of
these habitat requirements, the number of age 0+ fish that a reach of stream can support is
typically small relative to the average fecundity of an adult female steelhead. For example, a
female steelhead may produce, on average, about 5,000 eggs. Typical age 0+ densities in some of
the most productive California steelhead streams (e.g., tributaries to South Fork Eel River) have
been around 0.10 fish/ft2 (1.1 fish/m2) (Connor 1996). Therefore, with survival-to-emergence as
low as 25%, the number of fry produced from one female (5,000 x 0.25 = 1,250) may be
sufficient to fully seed the available rearing capacity of nearly 0.25 miles (0.4 kilometers) of
Upper Penitencia Creek at some of the highest densities observed in California. Consequently, the
reproductive effort may have little effect on the next generation’s adult population size (although
it may influence how many offspring from a particular female will occupy the finite number of
territories within a stream). Because of this, spawning gravel availability and egg mortality (e.g.,
as a result of poor gravel quality, redd dewatering, fungal infections, redd scour) may not have an
important effect on steelhead population dynamics. In other words, any density-dependent
mortality that might result from redd superimposition or density-independent mortality resulting
from redd scour and poor gravel quality (among other factors) may be irrelevant because, despite
3
Patterns described here are typical of North Coast and Central Valley populations, but may not necessarily reflect life histories of
steelhead in southern California. South of San Francisco Bay, where warmer stream temperatures and longer photoperiods may lead
to higher steelhead growth opportunities in some seasons, fish may achieve a suitable size for smolting at age 1+.
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these sources of mortality, far more fry are typically produced than can be supported by the
available rearing habitat. Therefore, the availability of suitable juvenile rearing habitat (either in
the summer or winter) is the factor that usually governs the number of steelhead smolts produced
from a stream. Consequently, we would expect that, even with small escapements and high egg
mortality, summer habitat will usually be seeded with steelhead fry.
Within the freshwater rearing stages of their life histories, the physical habitat requirements for
different age classes of steelhead are relatively similar, except that as fish age and grow their
requirements for space tend to become more restrictive. We postulate that age 0+ steelhead
rearing habitat, both summer and winter, did not typically limit steelhead production under
historical conditions and does not currently. Age 0+ steelhead can use shallower habitats and
finer substrates (e.g., gravels) than age 1+ steelhead, which, because of their larger size, need
coarser cobble/boulder substrate for velocity cover while feeding and escape cover from
predators. Because age 0+ steelhead can generally utilize the habitats suitable for age 1+
steelhead, but age 1+ steelhead can not use shallower and/or finer substrate habitats suitable for
age 0+ steelhead, it is unlikely that summer habitat will be in shorter supply for age 0+ than age
1+ steelhead. There may be stream systems or reaches where all available habitat is suitable for
both age 0+ and age 1+ steelhead, but even in these cases the density of age 0+ steelhead that the
habitat will support will be higher than for the larger age 1+ steelhead simply due to allometric
increases in territory size. In situations where summer habitat is suitable for both age classes,
competition for space between age 0+ and age 1+ steelhead may restrict the numbers of age 0+
steelhead that the habitat will effectively support. But in general, a reach of stream would
commonly support far fewer age 1+ than age 0+ steelhead in the summer.
As with summer habitat, a reach of stream will typically support far fewer age 1+ than age 0+
steelhead in the winter. In watersheds where temperatures become cold in winter (i.e., < 45°F),
predation risk becomes much greater because the fish become slower, sluggish, and less able to
escape predators. Refuge from high flows requires a similar type of habitat as concealment cover,
but may require access deeper into the streambed to avoid turbulent conditions near the surface or
even within first layer of substrate (the implications of this for embeddedness are discussed later).
During winter juvenile steelhead will often hide within the substrate (or other cover) during the
day, emerging only at night. In colder regions, juvenile steelhead may remain concealed in the
substrate all winter. Because steelhead tend to spawn in higher gradient reaches (i.e., >3%) with
confined stream channels, off-channel water bodies such as sloughs and backwaters are typically
rare. As a result, steelhead show less propensity then other species (e.g., coho salmon) for using
off-channel slackwater habitats in winter, and a greater propensity for using in-channel cover
provided by cobble and boulder substrates, which are typically common and usually immobile at
all but the highest flows in these areas. Because age 0+ steelhead are smaller and can utilize a
wider range of substrate than age 1+ steelhead, it will often be the case that there is more winter
habitat available for age 0+ than for age 1+ fish.
In watersheds where, as a result of anthropogenic disturbance, there are increased inputs of coarse
and fine sediment to the stream channel and decreased large woody debris, the disparity between
the amount of summer habitat for age 0+ steelhead and age 1+ steelhead is often increased. Pool
frequency is reduced with the removal of large woody debris, especially in forced pool-riffle and
plane-bed stream reaches. The remaining pools may become shallower as a result of aggradation
and the lack of scour-forcing features such as large woody debris. The filling of interstitial spaces
of cobble/boulder substrates by gravels and sand can affect summer habitat for both age 0+ and
age 1+ steelhead. But because of the larger size and more secretive nature of age 1+ steelhead,
their habitat will be reduced at lower levels of embeddedness than for age 0+ steelhead.
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Likewise, in the winter, habitat may often become unsuitable for age 1+ steelhead at lower levels
of sediment additions than for age 0+ steelhead. At higher levels of embeddedness, substrate will
become unsuitable for both summer and winter rearing, but it will often be more limiting in
winter because refuge from entrainment during winter freshets typically occurs deeper within the
substrate.
In the following section we use the existing available information as well as results from pilotlevel field studies conducted during spring and fall 2005 to evaluate this conceptual model.
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4
FOCUSED STUDIES
4.1
O. mykiss Abundance
4.1.1
Population Assessment
Information on historical fish species composition and distribution in Upper Penitencia Creek is
limited. It is generally thought that Upper Penitencia Creek is the main producer of steelhead for
the Coyote Creek basin (Li 2001, Smith 1998). Upper Penitencia Creek is one of only a few
creeks in the South Bay that support steelhead runs (Buchan et al. 1999) and is considered to have
the best steelhead habitat (SCBWMI 2003). To our knowledge, routine monitoring of fish
populations in Upper Penitencia Creek has not been conducted. In the past, several surveys have
documented the presence of steelhead in Upper Penitencia Creek, but have not quantified their
abundance. However, three sampling efforts conducted within the recent past have collected fish
data that is pertinent to a preliminary Upper Penitencia Creek steelhead population dynamics
analysis. The first of these efforts is smolt trapping conducted in Coyote Creek below the
confluence with Upper Penitencia Creek by SCVWD from 1998–2000. Smolts that emigrated
from Upper Penitencia Creek during the trapping period are assumed to have been caught in this
downstream migrant trap on their migration to the South Bay. In all years of trapping, Upper
Penitencia Creek was connected to Coyote Creek during the trapping period (J. Abel, SCVWD,
pers. comm., 2005). Since Upper Penitencia Creek is thought to be the primary producer of
steelhead in the Coyote Creek watershed, the majority of steelhead smolts captured in Coyote
Creek were likely produced in Upper Penitencia Creek, but the exact proportion in any year is
unknown.
The second source of steelhead abundance information is an electrofishing sampling effort
conducted in September 2000 (Li 2001). Li (2001) sampled during the period of low flow and
warm temperatures in late summer, after the period where any potential density-dependent
mortality or emigration of fish that had survived their first winter would have occurred. During
this effort, eight sites spaced at 0.5 mile (0.8 kilometer) intervals between stream mile 2.88 and
5.88 were sampled. Fish densities were estimated using multiple-depletion electrofishing in one
riffle and one pool at each of the sample sites, for a total of eight pools and eight riffles sampled.
Separate fish estimates were calculated for age 0+ and age 1+ and older steelhead for each habitat
type at each site. We used the densities reported by Li (2001) to extrapolate a population estimate
for the perennial reaches of Upper Penitencia Creek watershed between stream mile 3.5 and
barrier falls in Upper Penitencia Creek and Arroyo Aguague. Methods are described in Appendix
A-1.
The third source is from direct observation surveys conducted during this study. A total of 67
habitat units were sampled between stream mile 3.5 and barrier waterfalls in Upper Penitencia
Creek and Arroyo Aguague during May and October 2005. Age-specific fish densities were
estimated from direct observation using the “Method of Bounded Counts” (Figures 4-1 and 4-2)
and extrapolated population estimates were calculated (Figures 4-3 and 4-4) using the methods
described in Hankin and Mohr (in prep). Methods are described in Appendix A-1.
Collectively, this limited sampling record documents the density of multiple age classes of
juvenile steelhead during various seasons and years and presents a sparse but necessary starting
point for analyzing steelhead population dynamics in the Upper Penitencia Creek watershed. As
described in our conceptual model, age 1+ smolts may contribute very little to the number of
returning adult steelhead because they have very low ocean survival due to their small size. We
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believe it is essential to steelhead population viability in Bay Area streams to produce age 2+ or
older smolts, and that habitat suitable for producing them (age 1+ summer and/or winter) was
historically limiting and under disturbed conditions would become even more so. Therefore, the
initial focus of an investigation of steelhead population dynamics was to look at ratios of
abundance of different life stages. If the number of age 1+ steelhead during the late summer is
high relative to the number of age 2+ smolts, then an initial hypothesis would be that winter
habitat for age 1+ fish is limiting production of the next life stage. If the number of age 1+
steelhead is high during the late spring relative to the number of age 1+ during the late
summer/fall, then it would indicate that summer habitat for age 1+ fish is limiting production of
the next life stage. Finally, if the late summer/fall abundance of age 0+ steelhead is high relative
to age 1+ steelhead the following spring, then winter habitat for age 0+ fish is likely limiting
production of the next life stage (of course, this may also imply a limitation of 1+ winter habitat,
and increasing age 0+ winter habitat, but not age 1+ winter habitat would not result in an increase
in age 2+ smolts). The information available from existing data and recent field studies provide
“snapshots” of a dynamic cycle that influences population fluctuations over time. The precision
of both conceptual and parameterized models depends on the extent and quality of available
information. With streams such as Upper Penitencia Creek, where very limited historical
steelhead population information exists, conclusions must be considered preliminary and subject
to considerable uncertainty until information becomes available to test the assumptions upon
which they are based. Nevertheless, the existing information provides a beginning for testing the
hypotheses listed above.
The first step in our analysis of the Upper Penitencia steelhead population was to compare late
summer age 1+ steelhead estimates with numbers of age 2+ smolts. Although estimates of these
age classes of fish are not available for the same cohort, previous surveys provide snapshots of
fish abundance at various life stages from 1998 through 2000. During these three years, smolt
trapping was conducted in Coyote Creek below the mouth of Upper Penitencia Creek. In all three
years, smolt traps were in place for only a portion of the steelhead outmigration period, and
consequently the smolt totals undoubtedly underestimate total smolt production. This was
particularly true in 1998 when the trap was installed for only 13 days in May and 12 days in June
and 15 steelhead smolts were captured (Figure 4-5). The years of 1999 and 2000, when a total of
172 and 239 smolts were captured, respectively, provide the most complete record of smolt
production in the Coyote Creek watershed. During these years, traps were operated continuously
from early April through mid-June. While any smolts that had migrated during March would not
have been captured, the traps were in place during the typical peak smolt emigration period of
mid-April observed in other central and southern coastal California streams (e.g., Waddell Creek,
Santa Cruz Co., Shapovalov and Taft 1954; Lagunitas Creek, Marin Co., Bratovich and Kelley
1988; Arroyo de la Cruz, San Luis Obispo Co., Nelson 1994; Gazos Creek, San Mateo Co.,
Nelson 1994b). Scale analysis, completed in 2006 for a portion of the trapped smolts, indicates
that the majority of smolts were age 1+ (40%) and age 2+,(57%) with age 3+ and age 4+ fish4
comprising a small percentage of outmigrating steelhead (S.P. Cramer and Associates 2006).
To compare the number of age 2+ smolt numbers to the abundance of age 1+ fish during the late
summer, we first used the densities of steelhead observed by Li (2001) to calculate an
extrapolated population estimate for the area of stream between mile 3.5 and the barrier waterfalls
in Upper Penitencia Creek and Arroyo Aguague. This resulted in an estimate of approximately
4
Our aging system (see footnote 1, page 21) differs from that used by S.P. Cramer and Associates (2006) by one year. Our use of age
1+ is equivalent to S.P Cramer and Associates assignment of age 2; our use of age 2+ is equivalent to their assignment of age 3, and so
on.
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1,100 age 1+ and older steelhead in 2000 (see Appendix A-1 for extrapolated estimate methods).
Similarly, our snorkel survey in fall 2005 produced an estimate of approximately 1,475 age 1+
and older steelhead (Appendix A-1). If we assume that the majority of the smolts captured at the
Coyote Creek trap represent steelhead that reared in Upper Penitencia Creek and that age 1+
densities observed by Li (2001) and our 2005 survey are “typical”, the number of smolts observed
in 1999 and 2000 represent a small fraction of the late summer age 1+ and older steelhead
population in Upper Penitencia Creek. These estimates indicate an 85–90% reduction in
abundance of age 1+ fish during the winter, suggesting that a potential winter habitat bottleneck
exists for age 1+ steelhead. Since both resident and anadromous life histories are present in Upper
Penitencia Creek, we also must account for any age 2+ fish that remain in the rearing stream
either as residents or to smolt as age 3+ or 4+ fish. Based on our recent snorkeling observations
and population estimates (Appendix A-1), age 2+ and older fish comprised between 5 and 10 %
of the number of age 1+ and older steelhead present in the watershed and, consequently, this
relatively low percentage is not likely to affect our analysis.
Our interpretation of the existing data is relatively insensitive to some of the assumptions inherent
in the above discussion. For example, it is not likely that every steelhead smolt captured in the
downstream migrant trap in Coyote Creek reared in Upper Penitencia Creek. Additionally, Li
(2001) felt his sampling may have underestimated rearing potential in Upper Penitencia Creek,
since he was not able to access upstream areas thought to contain the best steelhead habitat (i.e.,
upstream of mile 6.0). Nevertheless, a similar population size was estimated using the results of
our snorkel surveys, which did include the anadromous fish bearing reaches of Upper Penitencia
and Arroyo Aguague above mile 6.0. However, if all smolts captured at the Coyote Creek trap
were not produced in Upper Penitencia Creek, or if Li (2001) and our surveys underestimate the
true number of age 1+ fish, then survival between these life stages may be even lower and would
indicate that winter habitat limitations may be even greater. Of course, if the smolt totals from
Coyote Creek dramatically underestimate the true number of smolts produced in Upper
Penitencia Creek, then winter habitat limitations may not be as severe. Our interpretation may be
fairly insensitive to underestimates of smolt production, however, since quadrupling the number
of age 2+ smolts captured still leads to a nearly 50% reduction between the late summer
abundance of age 1+ fish and the abundance of age 2+ smolts.
The second step in our analysis of steelhead population dynamics was to examine whether the
number of age 1+ steelhead is high during the late spring relative to the number of age 1+ fish
during the late summer/fall. If so, this may indicate that age 1+ summer habitat is limiting.
Abundance of age 1+ and older fish during spring 2005 and fall 2005 (Figure 4-2) indicates that
juvenile steelhead densities were fairly similar between these seasons. For example, during 2005,
the spring population estimate extrapolated from direct observation dives was approximately
1,300 fish (Appendix A-1), which is slightly lower but statistically not significantly different
from the fall estimate of approximately 1,475 fish. As mentioned previously, the fall estimate
derived from our snorkel survey is very similar to the estimate produced from electrofishing data
in Li (2001). If we consider these densities to be near a “typical” capacity for juvenile steelhead
production in the Upper Penitencia watershed, then this comparison indicates that summer habitat
is not the primary factor limiting steelhead populations under the conditions experienced by fish
in spring and fall 2005.
Finally, if the late summer/fall abundance of age 0+ steelhead is high relative to age 1+ steelhead,
then age 0+ winter habitat may be limiting production of age 1+ steelhead. Li (2001) probably
underestimates the number of age 0+ steelhead since sampling was conducted in downstream
reaches where abundance trends suggest that densities of age 0+ fish are among the lowest in the
watershed (Figure 4-1). Therefore, for this comparison, we rely on our fall 2005 estimate of age
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0+ steelhead, which was 2,489 fish. This compares to the spring estimate of age 1+ and older
steelhead of 1,300 fish. If we assume that the spring abundance of age 1+ steelhead that we
observed during this study is near the carrying capacity for fish during their first winter (i.e., age
1+ abundance provides a minimum estimate of the number of age 0+ fish surviving through their
first winter), then winter habitat for age 0+ fish limits the production of age 1+ steelhead.
However, it is unlikely that 0+ winter habitat ultimately limits steelhead population growth in
Upper Penitencia Creek, because of the previously described winter habitat limitations for age 1+
steelhead, (i.e., the abundance of age 1+ fish is much higher than the observed number of smolts
captured at the Coyote Creek trap).
In summary, spring and fall 2005 population estimates confirm that summer habitat does not
substantially limit the population of age 1+ and older steelhead. The available population
information indicates that winter habitat for age 1+ steelhead limits production of steelhead
during the freshwater rearing stages in the Upper Penitencia Creek watershed, which is consistent
with our conceptual model (Section 3.3). These conclusions are based on sampling conducted
within a single year and they should be interpreted with caution. The conceptual model and
preliminary evaluation of existing population data provides a tool for prioritizing focused studies
and a context for the interpretation of their results. The following sections presents the results of
focused field studies that attempt to link the hypothesized population dynamics described here to
current habitat conditions within the Upper Penitencia Creek watershed.
4.1.2
Population Modeling
A preliminary assessment of current habitat conditions for steelhead populations in the Upper
Penitencia Creek watershed was conducted within the framework of a population dynamics
model. This assessment relies on fundamental concepts in population dynamics, particularly
stock-production analysis. The assessment performed here was based on a combination of results
from field studies conducted by Stillwater Sciences and existing habitat data from Upper
Penitencia Creek (i.e., FAHCE 2000) and previous fisheries inventories (FAHCE 2000, Li 2001)
and is only intended to provide a preliminary, and conservative, indication of the degree to which
steelhead smolt production may be limited by current channel conditions.
The salmonid population modeling approach used in this analysis is based on stock-production
theory (Ricker 1976). Stock-production theory characterizes the number of individuals of one life
stage at one time (the production) as a function of the number in the same cohort of an earlier life
stage at an earlier time (the stock). This approach is particularly well suited to situations where
physical habitat is believed to be limiting, and where population dynamics can be plausibly
separated into density-independent and density-dependent components, such as productivity (the
ratio of stock to production that would be expected if there were no limits on population density)
and carrying capacity (the maximum number of individuals of a given life stage that the habitat
can support for the duration of that life stage). A detailed description of the population modeling
approach is described in Appendix A-2.
Mortality occurs at every stage within the life cycle of steelhead due to factors that may vary by
season and development (i.e., age and size) of fish. When considered in isolation, these factors
may not elucidate limits of the current watershed condition on steelhead population growth. For
example, in some situations improvement of summer rearing habitat may increase the abundance
of fish alive during that season, but if winter habitat limitations are greater, no population growth
will occur. In this study, our goal was to assess factors limiting the growth of the steelhead
population, rather than the abundance of steelhead at any given life stage. Therefore, the objective
of population modeling was to place results from selected focused field studies within the context
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of steelhead population dynamics through a preliminary modeling exercise. In the following
sections, results of selected focused studies are presented within this context.
4.2
Changes in Physical Habitat
Physical stream habitat is determined by basin-wide interactions between a number of variables,
such as geology, topography, vegetation, climate, hydrologic regime, and human activities that
can affect the quantity, quality, or timing of large woody debris (LWD), water, and sediment
inputs to the channel. Changes to these variables influence physical processes that control the
quality, abundance, and connectivity of habitat for steelhead and other aquatic and riparian
species in Upper Penitencia Creek.
We used historical data and field reconnaissance to identify changes in physical habitat that
occurred over the past 130 years, and to better understand the physical processes that control
sediment dynamics in Upper Penitencia Creek. Historical topographic maps and aerial
photographs indicate significant changes in land use from 1873 to 2005 (Figures 2-3 and 4-6).
These changes may have had substantial impacts to the physical processes that govern sediment
supply, transport, and deposition in Upper Penitencia Creek. Field observations confirm that the
creek’s channel has adjusted, and may still be adjusting, to the recent decades of urbanization and
other land uses in the watershed.
Arroyo de la Penitencia or Aguague, the earliest known name of Upper Penitencia Creek,
originally flowed from the Diablo Range into the San Francisco Bay near Milpitas, but was
diverted into Coyote Creek near the town of Murphy between 1873 and 1876 (Figure 4-6).
Downstream of the diversion, the creek still flowed into the bay, but was renamed Lower
Penitencia Creek, while the channel connected to Coyote Creek became Upper Penitencia Creek.
Examination of topographic maps and air photos reveals modest changes in channel planform
since the separation of Upper and Lower Penitencia Creeks, with most occurring before 1943.
The most conspicuous channel change was the emplacement of the Cherry Flat Dam in 1932 (see
Section 2.2). Other changes included the diversion of Silver Creek, which joined Upper
Penitencia Creek near Coyote Creek in 1899, to Coyote Creek, and the construction of an
irrigation canal near RM 3.0, both prior to 1943. Evidence of channel straightening in response to
infrastructure is apparent just downstream of Capitol Avenue, where in 1943 power transmission
lines intersected the channel, and by the mid 1970’s Interstate 680 crossed the creek along the
same path (USGS 1943; J. Abel, SCVWD, pers. comm., 2006).Despite these changes, the channel
length (21,650 feet [6,600 m]) of Upper Penitencia Creek below Alum Rock Park has remained
consistent since 1899 (Jordan et al. 2005).
Land use within the lower basin has changed from rural agriculture to mixed-use suburban on the
eastern edge of greater San Jose, the tenth largest city in the United States (pop. 905,000; City of
San Jose 2005). Early maps show the lower basin already divided into agricultural tracts by 1873
and occupied by the settlements of Murphy and Baker (Hoffman 1873, courtesy of SFEI). These
small settlements were swallowed by urban expansion that eventually spread across the entire
Santa Clara Basin. Low density rural structures interspersed among orchards were gradually
replaced by higher density residential and commercial buildings. The present day road network
grew out from Capitol Avenue, Berryessa Road, Mabury Road, and White Road, which were all
present (though not named) by 1899, with Interstate 680 being constructed in the 1950s. Greater
than 80% of the surface area of the lower basin is covered by recent urban growth, increasing
from less than 1% in 1899 (Jordan et al. 2005). With increases in impermeable surface area, the
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travel time of water from hillslope to channel decreases, and less water is able to percolate into
the soil, instead being directed through modern storm drainage systems into local stream
channels, such as Upper Penitencia Creek. This serves to increase the magnitude and shorten the
duration of flood peaks, causing flows to become more flashy.
Flood defense measures along the valley floor are a mix of earthen levees, arch and box culverts
that line 18% of the banks, and channel maintenance (Table 4-1). Channel maintenance is part of
a multi-year stream maintenance program that focuses on sediment removal, vegetation removal,
and bank protection to protect SCVWD facilities (EOA 2003). The defense measures have still
not prevented all floods, as water has inundated the adjacent area several times over the last
century, most recently in 1998 (HDR 2002). The Upper Penitencia Creek Flood Protection
Project, to provide protection from a 100 year event using natural flood protection design where
feasible, is currently in the planning stage (EOA 2003, SCVWD 2005). It is our understanding
that the SCVWD is proposing a flood protection design for all reaches downstream of Alum Rock
Park in partnership with the United States Army Corps of Engineers (J. Abel, SCVWD, pers.
comm., 2006). One alternative is to widen the existing channel along URB 5 to create a floodplain
within a setback of approximately 150 feet measured from the existing south bank (J. Abel,
SCVWD, pers. comm., 2006).
The channel modifications and channel maintenance influence sediment dynamics through
channel simplification that decreases roughness, thereby maintaining high water velocities and
increasing sediment transport capacity. Zones of channel incision, localized bank erosion, and
channel avulsion within the lower basin indicate channel adjustment to this modified sediment
transport regime. Knickpoints and migrating headcuts may have formed as fluvial processes
worked to balance transport with available sediment supply. The current sediment dynamics
indicate slight aggradational trend downstream of Alum Rock Park to King Road and channel
degradation downstream of King Road to Coyote Creek (PWA 2003).
Through Alum Rock Park the creek is also subject to channel modification. In the early 20th
century, visitors to the park recreated in mineral baths fed by spring water. Adjacent to the creek,
walkways and bridges sat atop rock walls lining both banks. Today, visitors use the park as a
hiking and picnic venue, yet the rock walls remain, and along with other channel modifications
(bank revetments sacked concrete, concrete walls, rock gabions, concrete crib walls) line 80% of
the channel length in the park (Table 4-2, BRG 2001). The rock walls have prevented natural
channel migration, the formation of floodplain surfaces and significant gravel bars, and the
recruitment of LWD from the banks. The structures have also increased water depth, causing an
increase in shear stresses on the bed and banks. Accordingly, the bed morphology is influenced
along reach by downcutting to shallow bedrock and the occasional grade control structures that
attempt to control bed elevation. The result is alternating stretches of boulder-cobble dominated
step-pools, empty reaches scoured to bedrock, and step-runs of sandy gravel (BRG 2001). The
dominance of large substrates indicates that the fine sediment load is quickly transported
downstream during high flow events, a process characteristic of a sediment starved channel (BRG
2001).
Large woody debris (LWD) is an essential ecological and geomorphic element in freshwater
systems. The basin occurs within a Mediterranean climate and few studies address the role and
dynamics (input and transport) of LWD within such systems. Most studies have been conducted
in temperate, coniferous systems. Nonetheless, in Mediterranean climates, LWD potentially plays
important roles in pool formation and nutrient retention (Gasith and Resh 1999). While logs
recruited to temperate systems tend to persist for long periods of time within the channel, forming
large jams lasting habitat features, Mediterranean systems recruit hardwoods (oaks, willows,
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laurel) that decay rapidly and rarely form large, persistent jams. The essential roles of LWD
within Mediterranean systems should be considered within the context of the wet-dry cycles that
occur within such systems. Mediterranean deciduous trees contribute leaf litter to the stream
channel in one short pulse in autumn, with minor contributions for lateral transport from the
banks over the remainder of the year. This allochthonous material is retained until the rainy
periods when seasonal floods occur, usually from winter to spring. The allochthonous input from
the riparian forest forms the energy base for aquatic ecosystems, but is rapidly flushed out during
rainy periods. Logs form debris dams that obstruct leaf litter, forming dense pockets of organic
material that can be processed by aquatic insects prior to downstream flushing. Logs also create
pools that can be used as winter refuge and as summer rearing habitat. In Mediterranean streams
that dry in the late summer and early fall, wood created pools provide a cool temperature refuge,
and maintain wetted sections that may be isolated due to channel drying.
The abundance and frequency of LWD in the Upper Penitencia Creek basin has likely been
impacted by historical land use changes. Wood in the upper portion of the basin is recruited
through landslides and mass movements. Input of wood may be influenced by land use that
changes forest character and also alters the rate of input from the hillslopes. Land use can alter the
extent of the forest, reducing the amount of potential wood available and the age, which
influences the size of LWD. The size of LWD is a significant influence on geomorphic function
(Ralph et al. 1994). Land use, such as grazing or road building can also increase the rate of LWD
input by increasing the occurrence of landslides.
Wood in the lower portion of Upper Penitencia basin would be recruited through bank erosion as
the channel meanders across its valley and floodplain. Surrounding land uses that reduce the
extent of the adjacent riparian corridor reduce the amount of available wood and channel
modification that reduces the occurrence of bank erosion, further preventing the recruitment of
wood. Channel confinement that prevents channel migration may also reduce the formation of
gravel bars and floodplains that are sites of LWD deposition. There is evidence of channel
modification (Table 4-1), channel straightening, and forest clearing due to land use (agriculture
and urbanization) along the lower portion of Upper Penitencia Creek. Fluvial transport from
upstream reaches can also be a significant source of wood to lower reaches where it deposits on
within the channel, on gravel bars, or along the banks. Accordingly, changes in land use upstream
influence wood loads downstream. Field reconnaissance found few pieces of LWD in the upper
basin. Wood was observed in Arroyo Aguague, but most had little effect on channel form, with
the exception of one fully spanning piece that stored gravel upstream and created a small cascade
downstream.
We observed few pieces of LWD downstream of the confluence of Arroyo Aguague and Upper
Penitencia Creek and through the park. This may have been caused by a lack of recruitment due
to channel confinement, or rapid flushing downstream. Few pieces of LWD were also observed in
the lower basin, but some recruitment via bank erosion did occur in URB 2 along the left bank.
We observed several areas of recent bank erosion, but LWD recruitment occurred in only one of
these areas. Woody debris loads are most likely reduced by a reduction in riparian forest, by a
lack of channel migration to recruit wood, and channel maintenance to reduce wood related
flooding (HDR 2002, J. Abel, SCVWD, pers. comm., 2006). The SCVWD historically removed
LWD to prevent flood damage, but currently leaves some wood in the channel to maintain aquatic
habitat (J. Abel, SCVWD, pers. comm., 2006). The reduction of woody debris may alter bed
morphology and stream hydraulics, resulting in fewer pools and reduced spawning gravel area.
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Table 4-1. Linear feet of modified and unmodified stream channel in Upper Penitencia Creek
(excluding Alum Rock Park).
General Channel Type
Detailed Channel Type
Length
(ft)
Total
(%)
Arroyo Aguague
Natural Unmodified
Natural Unmodified
43,359
49.6
Upper Penitencia
Natural Unmodified
Natural Unmodified
36,229
41.5
79,588
91.1
Creek
Total Unmodified
Upper Penitencia
Concrete Channel
Arch Culvert
72
0.1
Upper Penitencia
Concrete Channel
Box Culvert
593
0.7
Upper Penitencia
Earth Levee
Earth Levee
7,088
8.1
Total Modified
7,753
8.9
TOTAL FOR BASIN
87,341
100.0
Table 4-2. Linear feet of modified and unmodified stream channel in Alum Rock Park.
South Bank
Channel Type
(ft)
Total (%)
(ft)
Total (%)
1,960
15.1
3,251
24.9
1,960
15.1
3,251
24.9
Rock Wall
5,991
45.8
7,164
55.1
Revetment
288
2.2
1,570
12.1
Sacked Concrete
175
1.3
244
1.9
3,550
27.2
72
0.6
Bridge Abutment
496
3.8
587
4.5
Rock Gabions
57
0.4
116
0.9
Concrete Crib Wall
551
4.2
0
0.0
Total Modified
11,108
84.9
9,753
75.1
TOTAL
13,068
100.0
13,004
100.0
Natural Unmodified
Total Unmodified
Concrete Wall
4.3
North Bank
Sediment-Related Impacts on Salmonid Habitat
We assessed sediment-related impacts on salmonid habitat in the Upper Penitencia Creek
watershed by examining multiple factors, with emphasis on those that are: (1) known to affect
salmonid reproductive success directly, and (2) affected by land and water management in the
watershed. In addition, studies addressing these factors needed to be cost-effective and efficient
given the size of the study area and the limited time and funding available for this study.
Sediment-related factors evaluated during this study included the potential for:
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•
•
•
4.3.1
Reduced spawning gravel permeability (which reduces survival-to-emergence of
steelhead eggs);
Filling of pools (which reduces the quality and quantity of juvenile rearing habitat); and
Overwintering habitat quantity and quality (which affects the density of juvenile
steelhead that the stream can support during winter high flow conditions).
Spawning Gravel
The availability and quality of spawning gravel is a key factor influencing the spawning success
of anadromous salmonids. Successful spawning and incubation requires gravel of appropriate
size, without excessive levels of fine sediment. Gravel must also be distributed in patches large
enough to allow redd construction, and must be deep enough to allow excavation of an egg
pocket by the spawning fish. The key factor determining survival of salmonids during egg
incubation through fry emergence is sufficient flow of cool, oxygenated water through the
spawning gravels to ensure adequate delivery of dissolved oxygen and removal of metabolic
wastes. When a high percentage of fine sediment is deposited in or on the streambed, gravel
permeability can be substantially reduced. Gravel permeability and hydraulic head together
determine the rate of interstitial flow. Reduction of gravel permeability results in progressively
less oxygen and greater concentrations of metabolic wastes around incubating eggs and alevins
(newly hatched fish larvae or sac-fry) as they develop in the pore spaces between gravels,
resulting in higher mortality (McNeil 1964, Cooper 1965, Platts 1979, Barnard and McBain
1994).
We hypothesized that levels of fine sediment in Upper Penitencia Creek were elevated above
historical levels based on a review of existing information (i.e., PWA 2001 and 2003, FAHCE
2000, SCVURPPP 2002) and reconnaissance-level field assessments made by Stillwater Sciences
during February 2005, during which we observed that patches of suitably-sized spawning gravels
were frequently embedded with a mixture of sand and fine clay. Depending on the extent of the
fines and depth of spawning gravels, permeability could be poor in these areas, indicating that
regardless of the quantity of spawning habitat, the quality may be limited.
To assess spawning gravel quality in Upper Penitencia Creek, we combined an analysis of
existing information with focused field studies conducted during May 2005. We used
reconnaissance-level field surveys to validate estimates of spawning habitat quantity derived from
an existing habitat database (FAHCE 2000). Spawning habitat quality was assessed using
standpipe gravel permeability measurements that provide a rapid and cost-effective indicator of
both gravel quality and egg survival (Terhune 1958, Barnard and McBain 1994). Permeability5 is
preferred as a descriptor of spawning gravel quality because (1) it is the descriptor most directly
related to salmonid survival during egg incubation through fry emergence, and (2) it is affected
directly by fine sediment deposition. Measured permeability rates can be converted into an index
of predicted survival rates from egg deposition to fry emergence (i.e., survival-to-emergence
rates) using relationships derived from field observations of redds with differing permeabilities
(Tagart 1976) and studies where the permeability of artificial redds was manipulated
experimentally (McCuddin 1977) (Figure 4-7). Detailed methods are described in Appendix A-3.
The relative importance of egg survival to steelhead population dynamics, as affected by
spawning gravel permeability, was evaluated using a population model that incorporated input
5
Our use of the term ‘permeability’ (expressed in units of length/time), is consistent with the established convention in fisheries
biology. However the property being measured is more accurately termed ‘hydraulic conductivity,’ as defined in the hydraulics
literature.
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data from focused field studies, existing habitat measurements for Upper Penitencia Creek (i.e.,
FAHCE 2000), and values for habitat- and life stage-specific fish densities and survival rates
reported in fisheries literature (discussed in further detail in Appendix A-2). The model was run
using survival-to-emergence values ranging from 0–100%. The results of these variations in the
survival rate were expressed in terms of the fraction of smolts produced at a given survival rate
relative to the maximum potential production of smolts, given hypothetical 100% egg survival
(see Figure 4-8 and discussion below).
In considering spawning habitat quantity and quality, we focused our studies in the area
beginning upstream of Capitol Avenue (RM 2.2) and continuing to the waterfall fish barriers in
both Upper Penitencia Creek (RM 6.8) and Arroyo Aguague (0.8 miles upstream from the
confluence with Upper Penitencia Creek). The stream channel is intermittent in dry months
downstream of a point near the entrance to Alum Rock Park (RM 3.9), and is perennially wetted
throughout the park to the waterfall barriers. Because the entire stream channel is wetted during
the spawning and incubation period, it is conceivable that spawning may occur in areas
downstream of Dorel Drive. However, even if spawning is successful in this lower reach, in most
years emerging fry would face desiccation as the stream channel dried since numerous barriers
prohibit movement of young steelhead from ephemeral spawning habitats to upstream perennial
rearing habitats. Furthermore, even if juveniles could move into perennially wetted summer
rearing habitat, it is highly unlikely that unoccupied habitat would be available. The most relevant
findings of the spawning gravel analysis are discussed below. Detailed methods and results are
presented for the permeability studies in Appendix A-3 and for the population model in Appendix
A-2.
Spawning gravel patches as small as 2 ft2 (0.18 m2) may be used by resident rainbow trout
(Bjornn and Reiser 1991). During February 2005, we observed five redds in Upper Penitencia
Creek, ranging in size from 6–8 ft2 (0.6–0.7 m2) in area. Values reported in the literature for
average steelhead redd sizes are as high as 50 ft2 in large alluvial rivers (Bjornn and Reiser 1991)
but patches as small as 4 ft2 (0.37 m2) are used, especially in streams where spawning gravel
occurs in small isolated patches (Trush, B., McBain & Trush, pers. comm., 2004). Throughout
Upper Penitencia Creek, potential spawning gravel is distributed unevenly, with the highest
concentrations occurring in areas located 0.0–0.5 miles, and 1.7–5.4 miles from the mouth of
Upper Penitencia Creek (FAHCE 2000) (Figure 4-9). The total area of spawning gravel occurring
in patches 4 ft2 (0.37 m2) or larger from RM 0.0 to the waterfall barriers in both Upper Penitencia
Creek and Arroyo Aguague Creek, as reported by FAHCE (2000) and Stillwater Sciences 2005
data, is 15,841 ft2 (1,472 m2) (Table 4-3).
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Table 4-3. Number of potential spawning gravel patches greater than or equal to various size
classes in Upper Penitencia Creek upstream of RM 3.5.
Minimum Area
(ft²)
Number of Patches
4
386
10
237
15
167
20
138
30
101
40
80
50
68
Based on permeability measurements at 41 potential steelhead spawning sites, the median
predicted survival to emergence was 36%, with two of 41 sites having survival index values
lower than 25% and no sites having survival index values greater than 74% (Figure 4-10,
Appendix A-3) No longitudinal trends in gravel permeability were observed in Upper Penitencia
Creek, however median predicted survival to emergence was lowest in the two upper reaches,
UUP2 and AAG (Figure 4-11).
Shapovalov (1937, as cited in Shapovalov and Taft 1954, p. 155) found that survival to
emergence of steelhead eggs was 29.8% “in the presence of considerable silting” and 79.9% in
the absence of silting. Shapovalov and Taft (1954) hypothesized that under favorable conditions,
survival to emergence is high (70–85%) for steelhead eggs. From these results, we concluded that
our original hypothesis, that gravel permeability at potential spawning sites was insufficient to
support a high level of egg survival, is correct, and that elevated fine sediment concentrations in
the channel bed subsurface may adversely affect embryo survival in Upper Penitencia Creek.
The relative importance of egg survival to steelhead population dynamics, as compared with
factors such as the availability of rearing habitat for juveniles, was assessed via population
modeling using data from the permeability assessment and other focused field studies. The results
of the sensitivity analysis are illustrated in Figure 4-8. The analysis demonstrates that increases in
smolt production can be expected relative to increases in embryo survival only when embryo
survival is very low to begin with (e.g., lower than 10%). The response of the population to
improved embryo survival diminishes rapidly and even 10% survival is sufficient to produce
nearly 100% of the maximum number of smolts expected under optimum spawning habitat
conditions (i.e., maximum [100%] permeability) for Upper Penitencia Creek. Similarly, no
increases in smolt production would be expected by increasing spawning gravel quantity, since
population modeling indicated that greatly increasing fry production results in very small
increases in smolt production. These results strongly suggest that steelhead production is not
limited by spawning habitat quality or quantity in Upper Penitencia Creek.
Despite predictions of low egg survival, recent literature summaries (e.g., Buchan et al. 1999,
Leidy et al. 2003) and our spring and fall 2005 fish surveys have indicated that juvenile
steelhead/rainbow trout are common to abundant in Upper Penitencia Creek. This is consistent
with the results of our population modeling that indicate only limited spawning habitat is needed
to effectively seed the available rearing habitat in Upper Penitencia Creek. These findings are
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also consistent with empirical and theoretical evidence presented in our conceptual model for
steelhead in Section 3.3.
Despite the relatively weak link between spawning gravel quality and overall steelhead
population response, spawning gravel permeability is a useful tool for indicating sediment-related
impacts. Even if a target species, such as steelhead, is resilient to impacts of fine sediment in egg
stages, gravel permeability is a still a good measure of the degree of fine sediment intrusion into
gravels, and may detect anthropogenically elevated levels of fine sediment. The relative
importance of reduced permeability as compared with factors such as the availability of rearing
habitat for juveniles is discussed further in Section 5.
4.3.2
Pool Filling and Juvenile Rearing Habitat
Deposits of fine bed material (predominantly sand and fine gravels) may accumulate in pools
when the fine sediment load of a stream is high relative to transport capacity (Lisle and Hilton
1991, 1992; Hilton and Lisle 1993). These deposits reduce pool volume and potentially reduce
the amount of juvenile rearing habitat for steelhead, as well as for other fish and aquatic species.
In addition, reductions in pool depth may adversely affect thermal and velocity refugia and
reduce areas used for cover to avoid predators.
Pool filling often occurs when sediment supply is increased relative to the equilibrium conditions
in which the pool formed. The degree that pool filling will affect aquatic biota depends on several
factors. Pools in steeper channels are less likely to be filled with sediment because of their high
sediment transport capacity. Fine sediment deposition in pools, however, has been observed in
streams with gradients as high as 0.065 (6.5%) in areas with high sediment loads (Montgomery
and Buffington 1993, 1997). For aquatic organisms using pools as habitat, the depth of the pool is
more important than the proportion of the pool filled with fine sediment. Thus, larger pools with
greater average depths can usually bear a greater proportion of pool filling without loss of
summer rearing habitat. Filling of interstitial spaces in pool bottom substrates, however, could
still diminish summer habitat quality by reducing available cover for juvenile steelhead.
A measurement of the amount of pool filling with fine sediment is V*, the ratio of the volume of
fine sediment in a pool to the total pool volume (Lisle and Hilton 1991, 1992; Hilton and Lisle
1993). V* is an index of the mobile sediment within a stream channel and varies primarily as a
function of supply. V* also relates to spawning habitat quality, since mobilization of fine
sediment accumulations in pools can result in infiltration of redds constructed in the downstream
tails of pools, particularly those with high V* values (Lisle and Hilton 1991, Peterson et al.
1992). It should be noted that the summer V* measurement for a given pool can vary from year to
year in response to changes in sediment supply relative to transport capacity. Annual transport of
fine material depends more on the volume stored on the streambed than on the duration and
magnitude of streamflow (Lisle and Hilton 1999). Also, pool type does not significantly affect V*
measurements. Local mass wasting such as landslides and bank failures can also fill pools
temporarily until a sufficiently high flow scours the sediment. Lisle and Hilton (1999) found that
lithologies producing abundant fine bed material, such as sandstone components of the
Franciscan formation, were characterized by V* values greater than 10%. Values of less than
10% are considered low and a reference for undisturbed landscapes, while values of 10 to 20%
are considered moderate, and greater than 20% high (Kondolf et al. 2003).
We hypothesized that reduction of juvenile rearing habitat due to pool filling by fine sediment in
Upper Penitencia Creek was a potential problem given the distribution of fine sediments observed
during field reconnaissance in February and May 2005. Pool filling surveys were conducted in 21
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pools in Arroyo Aguague and Upper Penitencia Creek upstream of its confluence with Arroyo
Aguague and downstream through reach URB 2 during June 2005 (Map 4). For these studies, we
used a rapid method of assessing pool filling that was developed based on the methodology
described in Hilton and Lisle (1993). Like the original, the rapid V* assessment can be used to
compare changes in pool filling through time, yet requires one-tenth the field time investment. A
comparison of both methods found that the rapid method of assessing pool filling was
consistently within 10% of results using Lisle and Hilton’s V* method (Stillwater Sciences and
Dietrich 2002). A further discussion of the methodology for assessing pool filling and the detailed
results of the survey are presented in Appendix A-4.
The rapid V* assessment reveals that the mean level of pool filling in Upper Penitencia Creek
was 6.3% and the median was 5.5%, a low value (Kondolf et al. 2003). This refutes our original
hypothesis that pool filling is high in Upper Penitencia Creek. Five of the 21 pools surveyed had
more than 10% pool filling, while 10 of the pools had less than 5% fine sediment (Figure 4-12).
We did not observe a longitudinal trend in pool filling, nor did we observe a significant difference
between reaches (Figure 4-13). We did observe one pool with a value over 20%, but concluded
that local grade control, not a point source of sediment, contributed to the high value. The pool
was located in the ARP1 reach between two grade control structures that reduced local bed
gradient and water surface slope, resulting in a lowered sediment transport capacity (Lisle and
Hilton 1999). These findings indicate that pool filling by fine sediment is alone not likely to
adversely impact steelhead rearing habitat. Given that we observed a number of potential and
active sources of fine sediment delivery to the creek during field reconnaissance, the low
incidence of pool filling is probably due to the high transport capacity of the stream. The modern,
confined channel and hardened banks in portions of Upper Penitencia Creek within Alum Rock
Park (the primary rearing reach) have increased shear stresses on the bed particles, which
increases the sediment transport rate. As a result, most fine sediment is efficiently transported
downstream by low- to mid-level flows that occur relatively frequently.
Although pool filling may not limit rearing, other factors affecting the quality of pools may be a
factor limiting steelhead survival in Upper Penitencia Creek. Compared to other similar streams
in the Santa Clara Valley, pool frequency in Upper Penitencia Creek is high, but the pool area is
relatively low (Table 4-4). Field observations made in June 2005 indicate that the quality of pool
habitat for steelhead also decreases in the downstream direction though the urbanized reaches,
with little refuge for fish. The lack of LWD and the overall lack of channel complexity, as noted
throughout much of Upper Penitencia Creek, may be the primary factors responsible for the low
area of pools. Large woody debris has a major influence on creating fish habitat by scouring
pools and facilitating temporary sediment storage (Harmon et al. 1986). In plane bedded
channels, such as those found in the urban reaches, there are few channel obstructions to force
pool formation. Without flow obstructions or roughness elements, plane bedded reaches remain
relatively featureless and have little bed differentiation (Montgomery and Buffington 1997).
Thus, factors in addition to sedimentation may affect pool quality and potentially limit rearing
habitat for steelhead. Additional studies to document the summer rearing success of juvenile
steelhead in Upper Penitencia Creek, such as spring and fall population assessments, would
increase our confidence in these results.
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Table 4-4. Pool characteristics of selected streams in the Santa Clara Valley.
% Pool by Area
Number of Pools
(per 1,000 ft)
Alamitos Creek
0.38
3.3
Guadalupe Creek
0.50
7.6
Los Gatos Creek
0.57
3.1
Stevens Creek
0.49
6.3
0.25
6.5
Stream
Data from FAHCE (2000)
4.3.3
Winter Habitat Suitability
The availability and quality of overwintering habitat is an important factor influencing juvenile
survival and thus the production of steelhead smolts in many streams. Because steelhead
generally rear for more than one year in their natal stream, they are subject to harsh
environmental conditions during winter high flows. Despite the difficulties posed by winter
stream conditions, extended freshwater rearing may increase the chances of successful
outmigration and ocean survival. Research has shown that although age 1+ smolts may compose
a substantial portion of outmigrating steelhead, their survival is poor and they often contribute
little to the numbers of returning adults (Shapovalov and Taft 1954, Kabel and German 1967).
Survival of steelhead smolts tends to be much greater if outmigration occurs at age 2+ or 3+.
Persistence of a steelhead population is therefore highly dependent on the quantity and quality of
habitat for older age classes of juvenile fish (i.e., age 2+ and, to a lesser extent, 3+ and 4+).
Because larger fish have greater requirements for space and other resources, however, habitat for
age 1+ and older fish is usually more limited than for age 0+ fish.
Although features such as large woody debris jams may provide some value as winter refuge for
steelhead, cover consisting of interstitial spaces in cobble or boulder substrate is the key attribute
defining winter habitat suitability for juvenile steelhead (Hartman 1965, Chapman and Bjornn
1969, Meyer and Griffith 1997). As stream temperatures fall below approximately 45°F (7°C) in
the late fall to early winter, steelhead enter a period of winter inactivity spent hiding in the
substrate or closely associated with instream cover, during which time growth may cease (Everest
and Chapman 1972). Winter hiding behavior of juveniles reduces their metabolism and food
requirements and reduces their exposure to predation (Bustard and Narver 1975). In streams
where winter storms bring periodic high flows, juvenile steelhead also use coarse substrate as a
refuge from downstream displacement in high velocity flows. Velocity refugia may occur deeper
within the streambed than concealment cover typically used during winter base flows. Initial
observations from experiments conducted by Redwood Sciences Laboratory and Stillwater
Sciences in artificial stream channels indicate that juvenile steelhead respond to high flows by
seeking cover deep within cobble and boulder substrate. These experiments suggest that steelhead
will seek refuge at least 1–2 times the depth of the median particle size (d50) in unembedded
cobble/boulder substrate. Therefore, in streams subject to frequent winter storm events, the area
and depth of unembedded substrate may be a primary determinant of the winter carrying capacity
of juvenile steelhead.
Rearing densities for juvenile steelhead overwintering in high quality habitats with cobbleboulder substrates in California streams are estimated to range from approximately 0.24 fish/ft2
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(2.58 fish/m2 [W. Trush, McBain and Trush, pers. comm., 1997]) to 0.69 fish/ft2 (7.42 fish/m2
[Bjornn et al. 1977]). The density of fish that cobble and boulder substrate can support during the
winter declines when fine sediments fill the interstitial spaces of the substrate. Bjornn et al.
(1977) measured the densities of age 0+ steelhead (mean total length = 4.5 inches [11.4
centimeters]) remaining in laboratory stream channels with different substrate treatments to
evaluate the effects of sedimentation on winter habitat quality. At flows equivalent to winter base
flow, fine sediments were added to pools and riffles to embed the cobbles and boulders from 0 to
100%. Densities were between 0.65 and 0.74 fish/ ft2 (7 and 8 fish/m2) when cobbles and
boulders were completely free of fine sediment. Steelhead densities decreased to between 0.09
and 0.18 fish/ ft2 (0.97 and 1.94 fish/m2) when embeddedness increased to 50%. Densities
declined further to 0.05 to 0.06 fish/ ft2 (0.54 to 0.64 fish/ m2) when cobble and boulder substrate
were fully embedded. Similarly, Chapman and Bjornn (1969) found that approximately twice as
many juvenile steelhead remained in artificial stream channels with coarse substrate (“rubble”) as
in stream channels with gravel substrate when stream temperatures were below 50ºF (10ºC).
Meyer and Griffith (1997) found that the number of age 0+ rainbow trout (2.2–6.1 inches total
length [5.6–15.5 centimeters]) remaining in stream enclosures during the winter was higher when
the arrangement of cobble and boulder substrate provided the most refuge cover.
Previous studies of winter habitat use for steelhead and rainbow trout may overestimate winter
rearing densities for steelhead in coastal streams. These studies (i.e., Bjornn et al. 1977, Myer and
Griffith 1997) have been conducted in Rocky Mountain streams where, because of snowdominated precipitation, winter conditions consist of stable and relatively low streamflows.
However, habitat suitable for winter concealment cover is not necessarily suitable as refuge
during high velocity streamflows because of turbulent hydraulic conditions in the shallow
substrate. In areas with high winter streamflows, the number of fish the streambed can support
will likely be lower than reported for Rocky Mountain streams because deeper refuge habitat may
be less abundant than that required for winter concealment cover.
Observations conducted under conditions similar to high winter flows provide a clearer
understanding of the importance of interstitial velocity refuge. Results of preliminary experiments
by Redwood Sciences Laboratory and Stillwater Sciences in an artificial stream channel show the
effect of coarse substrate embeddedness on the use of interstitial space by age 0+ juvenile
steelhead during high (i.e., winter) flows. At flow velocities of 3–4 ft/s, densities of 0.65 fish/ft2
(7 fish/m2) were observed when cobbles were unembedded (Table 4-5) (Redwood Sciences
Laboratory and Stillwater Sciences 2004, unpublished). When cobbles were at least 30%
embedded in sand and finer particles, a lack of sufficient interstitial space precluded use by
juvenile steelhead of coarse substrates for refuge (i.e., a fish density of 0). Comparison of results
from this flume study and studies conducted under stable winter base flow regimes suggests that
completely unembedded coarse material provides similar carrying capacities during both base and
storm flows. However, with increasing fine sediment inputs carrying capacities for habitats
subjected to high winter flows decrease much more quickly than in habitats subject to stable
winter base flow.
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Table 4-5. Winter 0+ juvenile steelhead density (fish/ft2) in an artificial stream channel with
different levels of coarse substrate embeddedness.
Embeddedness
Steelhead Density (fish/ft2)
0%
0.65
10%
0.33a
20%
0.16a
≥30%
0
Source: Redwood Sciences Laboratory and Stillwater Sciences 2004, unpublished data
a
interpolated (not observed).
These studies demonstrate that the winter carrying capacity for juvenile steelhead depends
primarily on the amount of space located within the interstices of coarse substrate. Considerable
uncertainty remains about the rate at which winter habitat degrades with increasing fine sediment
loading. For example, results from Redwood Sciences Laboratory and Stillwater Sciences
(unpublished data) indicate that fish use declines to zero at embeddedness levels as low as 30%
(Table 4-5). However, it is not known if the decline in habitat capacity between zero and 30%
embeddedness is linear or takes the form of some other function.
Based on observations made during field reconnaissance and interpretations of existing
population information and formulation of conceptual model for juvenile steelhead, we
hypothesized that winter habitat may limit steelhead production. We combined an analysis of
existing information with focused field studies conducted during May 2005 to assess the quantity
and quality of overwintering habitat in Upper Penitencia Creek. Because juvenile steelhead
require low velocity habitat in the winter and are known to seek refuge in the interstices of coarse
substrates during periods of high flows and low temperatures, we focused our winter habitat
assessment on habitats composed of cobble and/or boulder substrates in the perennial rearing
reaches of Upper Penitencia Creek between mile 3.5 upstream to barrier waterfalls in Upper
The assessment of winter habitat availability in Upper Penitencia Creek did not include relatively
rare habitat features such as large woody debris jams, root wads, and backwater habitat. Juvenile
steelhead are known to use these habitats to some degree during winter (Hartman 1965, Swales et
al. 1986, Raleigh et al. 1984, Fontaine 1988). Although these habitats were not commonly
observed in Upper Penitencia Creek, we may have underestimated winter habitat availability by
not including them in our analysis. Information on substrate area was obtained from the existing
FAHCE (2000) database. Substrate embeddedness was determined during field studies conducted
by Stillwater Sciences. For those habitat units containing cobble and/or boulder as either the
dominant or subdominant substrate, substrate embeddedness was estimated by removing several
sediment particles (i.e., cobble or boulder) to determine the percentage of the circumference that
had been inundated by smaller sediments. A slight discoloration of the particles is typically
apparent above and below the level of embeddedness (Sylte and Fischenich 2002).
Winter habitat area, estimated by summing the area of cobble and boulder substrate, is 120,741 ft2
(11,217 m2) upstream of RM 3.5. The area of winter habitat represents approximately 52% of the
total wetted area in the primary rearing reach of Upper Penitencia Creek, as determined by
FAHCE (2000) habitat survey data collected during summer 1998 and/or 1999. The distribution
of winter habitat is relatively even, with an upstream increasing dominance of boulder habitat in
reaches with step-pool features (Figure 4-14). However, the existing database is likely to
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40
overestimate the true winter carrying capacity for Upper Penitencia Creek. The FAHCE habitat
survey was not conducted with the intent of estimating the area of coarse substrate suitable for
winter refuge habitat. The size range of cobble substrate includes smaller particles (64 to 90 mm)
than would be considered suitable for juvenile steelhead overwintering (i.e., >90 mm). Therefore,
winter habitat area may be substantially different than this total depending on the size distribution
of the cobble substrate present (although this distribution is unknown).
A relatively small percentage of the cobble and boulder habitat area in Upper Penitencia Creek
was considered suitable for overwintering habitat (Appendix A-5). Interstitial spaces found in
coarse substrate were typically lacking due to a high degree of embeddedness by fine sediment
(i.e., small gravel, sand, and silt). Mean cobble and boulder substrate embeddedness was
approximately 28% (range 10–60). In cases where surface embeddedness was relatively low (i.e.,
10%), embeddedness of subsurface layers of coarse substrate were high (50–80%) (Appendix
Table A5-1). We estimated winter rearing densities in Upper Penitencia Creek using a weighted
average of cobble/boulder area and fish densities (Table 4-5) corresponding to the level of
embeddedness observed in habitat units surveyed during focused field studies (Appendix A-5).
Based on this relationship, the average winter rearing densities in Upper Penitencia Creek were
estimated at approximately 0.034 fish/ft2 (0.37 fish/m2) for age 0+ steelhead and 0.010 fish/ft2
(0.11 fish/m2) for age 1+ steelhead. We used the estimates of rearing densities and habitat area to
compare with observed fish densities from spring and fall 2005 and previous fisheries surveys in
Upper Penitencia Creek to allocate the available winter habitat between multiple steelhead age
classes (Appendix A-5). Based on these estimates we assigned approximately 48,061 ft2 (4,465
m2) of the available cobble/boulder habitat to age 1+ steelhead, and 44,349 ft2 (4,120 m2) to age
0+ steelhead. This resulted in approximately 20% of the cobble/boulder area estimated by
FAHCE (2000) being removed from the winter habitat area estimate. Using these habitat areas
and rearing densities estimated from substrate embeddedness levels to estimate carrying
capacities results in close agreement with the fish population estimates derived during spring and
fall 2005 and previous fish surveys (Appendix A5).
Cobble and boulder substrate was often organized laterally in a series of steps that create
localized areas of suitable winter habitat, but the majority of coarse material was typically
embedded in a matrix of finer gravel, sand, and silt. In addition, although localized conditions
resulted in an unembedded surface layer in some areas, this condition rarely, if ever, extended
more than a single layer deep into the stream bed. As mentioned above, Meyer and Griffith
(1997) observed that the arrangement of cobble and boulder substrate influenced the carrying
capacity of the substrate, with higher fish densities observed when cobbles were touching than
when they were not touching. Additional experimental observations also indicate that successful
refuge from high flows requires sufficient depth of these larger substrates (Redwood Sciences
Laboratory and Stillwater Sciences, unpublished data). The high levels of embeddedness
observed in Upper Penitencia Creek probably results in a relatively low winter carrying capacity
for juvenile steelhead. The high embeddedness we observed may be at least partly the result of
the naturally high sediment load in the basin (see Section 2.3). Other indicators of fine sediment
storage (i.e., gravel permeability, pool filling) do not indicate an imbalance of supply and
transport. However, the sensitivity of fish populations to winter habitat quality is consistent with
our conceptual model (Section 3.3) that postulates that winter habitat may have been a
historically important factor limiting steelhead populations, and may be particularly sensitive to
impacts of human land use. However, at this time we cannot differentiate between reference and
current conditions.
The relative importance of winter habitat quality to steelhead population dynamics, as compared
with factors such as the quality of spawning habitat, was assessed via population modeling using
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habitat data from FAHCE (2000) and the results of our focused studies. The relative importance
of winter habitat quality to steelhead population dynamics, assessed over a range of winter habitat
fish densities, is illustrated in Figure 4-15. The purpose of this analysis was to determine the
sensitivity of steelhead populations to a range of winter habitat qualities relative to habitat
availability as a constraint on population growth. The results of these variations in fish density
were expressed as the fraction of smolts produced at a given winter fish density relative to the
maximum potential production of smolts, given a high fish density (Figure 4-15). The analysis
demonstrates that increases in the quantity or quality of winter habitat are expected to result in
dramatic increases in smolt production when habitat quality is low to begin with. For example,
increasing winter habitat rearing densities for age 1+ steelhead from 0.01 to 0.05 fish/ft2 (0.11 to
0.54 fish/m2) results in an approximately 65% increase in smolt production (assuming densities of
age 0+ steelhead increase proportionally; Figure 4-15). These results also indicate that if our
current estimate of winter rearing densities is reasonable, any decrease in winter habitat quality
could result in substantial reductions in steelhead production. However, we urge caution in
applying this preliminary modeling analysis, which is based on assumptions about survival rates,
fish densities, and habitat use in Upper Penitencia Creek as well as from other stream systems.
The lack of information specific to Upper Penitencia Creek adds some uncertainty to our
conclusions. Studies to document actual juvenile densities at the beginning and end of winter over
several seasons would be very useful in validating our assumptions and the modeling results.
4.4
Fish Passage Barriers
Barriers and impediments to fish movement can cause significant adverse impacts on anadromous
fish populations by restricting the ability of fish to leave and return to the basin and the ability of
rearing juveniles and resident adults to access habitat and track resources within the system. By
disrupting habitat connectivity, even a small number of barriers can have a disproportionately
large impact on a population if the barriers obstruct access to large amounts of habitat or habitat
of critical importance.
Potential fish passage barriers and impediments were identified by FAHCE (2000) as a
significant factor limiting habitat availability and quality for salmonids in the Coyote Creek
system. Although the spatial extent and temporal duration to which barriers and impediments
impede access to habitat in Upper Penitencia Creek is largely unknown, the documented presence
of anadromous O. mykiss (i.e., steelhead) adults (CDFG 1987) and smolts (Smith 1997) in the
creek indicates that adults successfully ascend to suitable spawning habitat and reproduce in at
least some years. The ability of adult steelhead to access all suitable habitat, however, especially
in upstream reaches, is dependent on the extent to which structural and flow-related barriers
impede upstream passage. Because of the limited ability of juveniles to disperse upstream,
especially under extreme high or low flow conditions, limited access to spawning habitat can be
expected to also limit the amount of available rearing habitat. Access to downstream rearing
habitat may be similarly limited by flow-related barriers. By disrupting habitat connectivity,
barriers may limit the ability of rearing juvenile steelhead to access high quality rearing habitat
and can prevent smolts from outmigrating.
Flow influences the degree to which structural impediments are passable by adults moving
upstream and, to a lesser extent, by smolts and juveniles moving downstream. High flows may
pose problems for upstream migration if water velocity at artificial structures and fish passage
facilities exceeds that which can be overcome by the fish. Low flows may render structures
impassible if water depth is too shallow to allow movement of fish over or through the
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impediment. Fish ladders can become impassible if flow is not sufficient to provide flow through
the steps, or if resting pools or downstream jump pools are too shallow. No quantitative analysis
has previously been conducted to determine the amount of habitat rendered inaccessible by
barriers or the effects of potential delays in upstream or downstream passage by steelhead.
The potential impacts of structural and flow-related barriers on steelhead in Upper Penitencia
Creek are evaluated below. Results of these analyses were used to examine the possible effects of
fish passage barriers on the steelhead population in Upper Penitencia Creek.
4.4.1
Structural Fish Passage Barriers
In-channel structures such as flow diversion weirs, grade control structures, and road crossings
may create steep drops or wide expanses in the channel that cannot be jumped by fish. In
addition, these and other structures may artificially reduce water depth to a point that precludes
fish passage or may concentrate flows to such a degree that fish cannot overcome the current to
move upstream. In an attempt to allow upstream passage by adult salmonids, some in-channel
structures incorporate passage facilities (i.e., fish ladders). The effectiveness of passage facilities,
however, may be reduced at very high or low flows, or when they become clogged with sediment
and debris. Even barriers that fish are able to pass after some effort (i.e., impediments) may be
significant if the level of effort required exhausts the fish and reduces reproductive fitness or
longevity.
Although most attention is typically focused on barriers to upstream passage, some structures
may also impair downstream movement of juvenile salmonids or outmigrating smolts, especially
at low flows. In addition to limiting downstream passage of outmigrating steelhead smolts and
potentially delaying outmigration, structural barriers may also curtail movement by juveniles,
thereby reducing the amount of available rearing habitat. The number of potential barriers to
juvenile movement and the extent to which access to rearing habitat is limited are highly
dependent on several factors, including the location of emergence, the quantity and quality of
nearby rearing habitat, and flow duration and magnitude. Flow-related (i.e., non-structural)
barriers are discussed in Section 4.4.2 below.
Relatively few structures in Upper Penitencia Creek have been identified as potential barriers to
fish passage. Existing data and observations made during field reconnaissance indicated that none
of the documented artificial impediments in Upper Penitencia Creek act as complete barriers to
fish passage during peak periods of upstream migration by adult steelhead or outmigration by
juveniles. Previous investigations have indicated that there are no physical barriers to upstream
migration of anadromous fish from San Francisco Bay to the Upper Penitencia Creek watershed
(Buchan et al. 1999). Under typical flow conditions during the primary period of upstream
migration (January–April), it appears highly likely that Upper Penitencia Creek and Arroyo
Aguague are accessible to steelhead as far upstream as the natural waterfalls. Although low flows
may at times prove problematic for outmigrating steelhead smolts (Smith 1998), we could find no
evidence that structural impediments prevent downstream movement during the primary
outmigration period (February–May). Based on this information, we hypothesized that instream
structures do not have a substantial impact on habitat connectivity in Upper Penitencia Creek, and
are therefore not expected to limit production of steelhead or successful emigration to Coyote
Creek.
The historical and presumed current upstream limit of fish passage in the Upper Penitencia Creek
watershed is defined by the natural waterfalls located in Upper Penitencia Creek and Arroyo
Aguague upstream of their confluence (Map 1). The waterfall in Upper Penitencia Creek (Figure
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3-1) is located approximately 6.8 miles (11 kilometers) upstream of the Coyote Creek confluence
and 0.1 miles (0.1 kilometers) upstream of the confluence with Arroyo Aguague. The waterfall in
Arroyo Aguague (Figure 3-1) is located approximately 0.8 miles (1.3 kilometers) upstream of its
confluence with Upper Penitencia Creek. Both are considered to be complete barriers to upstream
fish passage (FAHCE 2000, Buchan et al. 1999, others). Cherry Flat Reservoir, located near the
headwaters of Upper Penitencia Creek, approximately 2.3 miles (3.7 kilometers) upstream of the
waterfall, therefore has no effect on fish passage.
Downstream of the waterfalls, several artificial instream structures in Coyote Creek and Upper
Penitencia Creek may act as fish passage impediments. FAHCE (2000) lists seven partial fish
passage barriers (impediments) in Coyote Creek downstream of the Upper Penitencia Creek
confluence. In Upper Penitencia Creek and Arroyo Aguague downstream of the waterfalls, only
one documented structural impediment currently exists (FAHCE 2000, SCVWD 2002) (Table 46, Map 1). This structure, a concrete grade control weir, or drop structure, is located in Alum
Rock Park adjacent to the Youth Science Institute (YSI) (Figure 4-16), approximately 5.9 miles
(9.5 kilometers) upstream of the confluence with Coyote Creek. It has been identified as a
potential barrier to upstream migration at low flows (FAHCE 2000, Buchan et al. 1999, CDFG
1987) and assigned a high priority for removal (FAHCE 2000). An additional, previously
documented impediment, the low-flow crossing at Quail Hollow in Alum Rock Park, was
removed and replaced with a clear span pedestrian bridge in 2004. A complete list of documented
barriers and impediments is presented in Appendix A-6.
Several other artificial structures in the creek may interrupt habitat connectivity during low flows
and potentially impede downstream passage by juveniles and smolts. These include the diversion
structures at Noble Avenue (RM 3.6) and Mabury Avenue (RM 1.3). Although both structures
have fish ladders and have been deemed passable by upstream-migrating adult steelhead, their
effect on habitat connectivity and fish passage at low flows has not been documented. Smith
(1998) stated that the ability of steelhead smolts to reach Coyote Creek may be limited by low
flows downstream of the Noble Avenue diversion, but gave no specific information regarding
structural impediments to outmigration. Observations made by Stillwater Sciences during six
separate field reconnaissance and focused study surveys conducted from January–May, 2005
indicated that flows were suitable for downstream passage at these structures. Flow conditions
during these surveys, however, were not necessarily representative of the full range of flows that
could potentially occur in Upper Penitencia Creek during the steelhead outmigration period.
Table 4-6. Documented fish passage impediments and barriers in Upper Penitencia Creek, up to
and including the natural waterfall.
a
b
River
Milea
Barrier
IDb
Description
Barrier Typeb
0.0
GB1
Critical riffle at Coyote Creek confluence
Partial; non-structural
2.0
GB16
Critical riffle at HWY 680 crossing
Partial; non-structural
5.9
GB18
6.8
GB9
Grade control structure at Youth Science Institute
(YSI), Alum Rock Park
Natural waterfall in Upper Penitencia Creek,
upstream of confluence with Arroyo Aguague
Partial; structural
Complete; structural
(natural)
river mile upstream of Coyote Creek confluence; from FAHCE (2000) or GIS data (SCVWD 2000)
Barrier ID and type (degree) from FAHCE (2000) and SCVWD (2002)
We evaluated the physical characteristics of the YSI drop structure (Barrier GB18) to assess the
likelihood that it impedes upstream movement by steelhead. The combination of a potential
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barrier’s geometry, the hydraulic conditions, and the leaping ability of the fish determine the
likelihood of fish passage. The angle of the fish’s leap, as well as the depth of the takeoff pool
and the water depth at the landing location are among the critically important factors for
determining passage at a potential barrier (Powers and Orsborn 1985). Passage conditions are
optimized when (1) the depth of the plunge pool is equal to or greater than the length of the fish,
(2) the water depth at the falls crest is greater than the fish’s body depth, and (3) the water
velocity at the crest is less than or equal to the sustained swimming speed of the fish (Powers and
Orsborn 1985). Steelhead have a maximum sustained swimming speed (also called cruising
speed) of 4.6 ft/s (Bell 1973).
Measurements were taken at the YSI drop structure on 31 May 2005, when streamflow at the
SCVWD Dorel gage (SF 83) was 2.0 cfs (SCVWD 2005) (Table 4-7). Water velocity at the falls
crest (the lip of the structure) was not measured, but it was estimated to be well below the critical
threshold of 4.6 ft/s. We compared the measured vertical and horizontal dimensions of the YSI
structure with the steelhead “leaping curves” developed by Powers and Orsborn (1985) to assess
the likelihood of upstream passage (Figure 4-17). The curves represent leap distances for three
different takeoff angles and two fish condition factor coefficients (Cfc6).
Table 4-7. Measured characteristics of the grade control drop structure located at the Youth
Science Institute in Alum Rock Park (GB18).
Characteristic
Measurement*
Vertical distance from plunge pool water surface to falls crest
5.1 ft
Horizontal distance from plunge to falls crest at lip of structure
6 ft
Depth of plunge pool (takeoff)
3.3 ft
Water depth at falls crest
0.3 ft
Depth of pool at top of structure (landing)
0.8 ft
* measurements taken on 31 May 2005; discharge at Dorel gage was 0.51 cfs
This analysis indicates that the YSI drop structure is easily passable by steelhead with a Cfc of
1.0 (solid curves in Figure 4-17) at the flow measured (approximately 2.0 cfs). As shown in
Figure 4-17, a steelhead with Cfc = 1.0, leaving the water at a 60° angle, can clear an obstacle
eight feet (2.5 meters) high and over 17 feet (5.2 meters) wide. Steelhead attempting to leap the
structure are expected to have a Cfc close to 1.0 (the strongest, healthiest fish), due to the
relatively short, 16 mile (25.7 kilometer) travel distance from salt water. Depth of the takeoff and
landing pools was adequate at the flow measured, but the shallow water depth at the falls crest
(0.3 ft [0.09 m]) could present a problem for leaping steelhead at similar or lower flows if the
horizontal leaping distance is insufficient to clear the crest. Given the horizontal range of a
leaping steelhead, however, this seems unlikely. Furthermore, the measured depth of the pool at
the top of the YSI structure, just upstream of the falls crest, was 0.8 ft (0.24 m) (Table 4-7), which
exceeds the minimum upstream passage depth of 0.6 ft (0.18 m) reported by Thompson (1972)
for an adult steelhead. It can be expected that a leaping steelhead would be able to clear the falls
crest and land upstream in the deeper pool.
6
The coefficient of fish condition (Cfc) referenced here is a subjective measure based on observations of fish condition by Powers and
Orsborn (1985) for coho and chum salmon. It does not correspond to the condition factor commonly used in fisheries biology, which
is based on measured length and weight. As defined by Powers and Orsborn (1985), a fish with Cfc = 1.0 is a “bright” fish, fresh out
of salt water, with no visible spawning colors. A fish with Cfc = 0.75 is a fish in “good” condition, in the river for a short time, with
spawning colors apparent.
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Water depth and velocity at the landing location are potentially critical uncertainties that vary
with flow. Although it was not feasible as part of this analysis to measure water depths and
velocities during all potential passage flows, the hydraulic characteristics at the YSI drop
structure are such that only at the highest flows would the water velocity at the top of the
structure be expected to approach the critical sustained steelhead swimming velocity of 4.6 ft/s.
Depth and velocity measurements taken at a range of high and low flows during the primary
period of steelhead upstream migration (January–April) would be required to verify this
supposition.
Adult steelhead that successfully surmount the YSI drop structure in Alum Rock Park have access
to the full extent (7.5 miles [12 kilometers]) of habitat in Upper Penitencia Creek and Arroyo
Aguague downstream of the waterfall barriers. Existing data indicates, however, that suitable
rearing habitat for O. mykiss is primarily located upstream of RM 3.5. If the YSI structure
prevents access to upstream reaches, nearly 1.5 miles (2.4 kilometers) of stream habitat becomes
unavailable. Steelhead would then be restricted to 50% of the pool area, 74% of the spawning
area, and 31% of the cobble/boulder overwintering habitat that would otherwise be available
upstream of RM 3.5 (Figure 4-18). Only pools less than two feet deep (<0.6 meters) were
considered in this analysis.
The impact of this habitat limitation is determined largely by the quality of the habitat located in
the uppermost 1.5 miles (2.4 kilometers) of the creeks. This is best illustrated by the estimated
steelhead smolt production in this reach, compared with habitat downstream of the YSI structure.
We evaluated the potential effects of limited access to spawning and rearing habitat on the
steelhead population using stock-production based population modeling. Using the amount of
available spawning, rearing, and overwintering habitat in Upper Penitencia Creek and Arroyo
Aguague upstream of RM 3.5 as a baseline, we assessed the relative impact of blocked upstream
passage at the YSI drop structure. If upstream access is blocked by the YSI structure located 5.9
miles (9.5 kilometers) upstream of the Coyote Creek confluence, the fraction of potential smolt
production is reduced to 0.5, a reduction of 50% relative to the maximum potential smolt
production in Upper Penitencia Creek and Arroyo Aguague between RM 3.5 and the natural
waterfall barriers. This analysis assumes that juvenile steelhead have unimpeded access to habitat
in the creek upstream and downstream of the location where they were spawned. More detail on
the steelhead population assessment is presented in Section 4.5, and a detailed description of the
population model is presented in Appendix A-2.
The results of this analysis indicate that the YSI drop structure, if it in fact prevents upstream
passage, can substantially limit the potential steelhead production in the Upper Penitencia Creek
watershed. Based on our analysis of steelhead leaping ability, however, the likelihood of
upstream passage at the YSI structure is high, and it is therefore not believed to limit the amount
of habitat accessible to steelhead. Additional data are necessary, however, to validate this
assessment. Limited information is available to support a conclusion regarding potential
downstream passage limitations posed by instream structures. Despite our observations made
during the relatively wet spring of 2005 indicating that suitable flows for downstream passage
were frequently present at instream structures, the lack of information from dryer years prevents a
positive conclusion. We therefore cannot accept or reject our hypothesis that structural barriers in
Upper Penitencia Creek likely do not limit steelhead production.
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4.4.2
Flow-related Barriers
In addition to structural barriers, natural variations in precipitation and runoff, together with
reservoir releases, diversions, and water returns, influence the amount of flow and suitability for
fish passage in Upper Penitencia Creek. While upstream spawning migration by anadromous
salmonids typically occurs during the wet season when flows are generally sufficient (unless the
onset of rains is late), inadequate flows in the spring can pose a potentially significant barrier to
fish movement within the stream and to smolts emigrating to the ocean. Dry reaches can impact
juvenile steelhead at other times of the year by preventing or restricting access to habitat during
the rearing period. Upstream passage can also be restricted by high flows, especially at instream
structures where flow is concentrated. Based on a review of available information, we
hypothesized that flow-related barriers, either alone or in conjunction with potential structural
barriers, can substantially limit summer rearing and outmigration success by steelhead in Upper
Penitencia Creek. This potential limitation may have been a natural occurrence in the lower
reaches of the creek, but given the lack of historical stream flow data our analysis focused on the
effects of current flow patterns.
Flow in Upper Penitencia Creek originates largely from springs and tributaries, most notably
Arroyo Aguague, its primary perennial tributary. Releases from Cherry Flat Dam are typically
made only during dry periods when additional water is required to maintain flow downstream.
The City of San Jose, which owns and operates Cherry Flat Dam, is required under a California
Department of Fish and Game (CDFG) 1600 permit to maintain a “wet/active” channel
downstream of the dam (Buchan et al. 1999). It is not clear from existing information, however,
how far downstream this requirement applies, and whether the permit stipulates release amounts
or timing. Several authors have reported that portions of Upper Penitencia Creek downstream of
Alum Rock Park are intermittent or subject to seasonal drying during summer (EOA 2003,
SCBWMI 2003, Buchan et al. 1999, Smith 1998, HRG 1992).
Potential flow-related passage barriers identified in Upper Penitencia Creek include two “critical
riffles” where channel geometry may limit fish passage at low flows due to shallow water depth
or drying of the channel (FAHCE 2000) (Table 4-6). Additional low-flow passage constraints
resulting from water diversions and seasonal drying may also exist downstream of Dorel Drive.
Diversion locations in this reach include: (1) the Noble Avenue diversion (RM 3.6) (2), the
Penitencia Creek Park diversion (RM 1.7), and (3) the Mabury Avenue diversion (RM 1.3). No
information was available regarding operation of the Penitencia Creek Park diversion.
At the Noble Avenue diversion, a portion of stream flow is diverted to the three percolation ponds
located nearby on the north side of the creek. The percolation ponds also receive water from the
South Bay Aqueduct (EOA 2003, SCBWMI 2001). Diversion typically occurs from April–
October (SCVURPPP 2003a), but the ponds are operated year-round (J. Abel, SCVWD, pers.
comm., 2006). Water from the ponds is discharged back into the creek for instream percolation.
Although imported water discharged from the percolation ponds may at times augment
streamflow as far as two miles (3.2 kilometers) downstream of the ponds (Smith 1998), this water
can be relatively warm. CDFG (1987) reported that effluent from the percolation ponds provided
the majority of the flow in the creek downstream of the ponds, and that the water entering the
creek from the ponds was 3° F warmer (67° F) than the creek water upstream of the ponds (64°
F). The date of these observations, however, was not reported. The USACE (1995) reported that
Upper Penitencia Creek between King Road and the Coyote Creek confluence often dries in late
summer/early fall. Furthermore, Smith (1998) noted that water imports from the South Bay
Aqueduct are subject to occasional cutoffs, causing the creek to go dry and posing problems for
smolt outmigration from April–June. Existing information was not sufficient to determine the
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amount, timing, or frequency of these occurrences, but Smith (1998) stated that sufficient flows
for smolt outmigration during April and May are likely to occur only in wet years.
Farther downstream, water is again diverted at the Mabury Avenue diversion (RM 1.3) to a
percolation pond on the south side of the creek. This diversion is typically operative from April–
October (SCVURPPP 2003a) but may also be operated at other times of the year (J. Abel,
SCVWD, pers. comm., 2006). Upper Penitencia Creek downstream of the Mabury Avenue
diversion is classified as intermittent (EOA 2003) due in part to summer diversion of water at this
location. We could find no information regarding return flows to the creek from this percolation
pond.
In addition to the diversions discussed above, a “dryback zone” at RM 1.5 was identified by
FAHCE (2000). No additional information was found describing the features of this dryback
zone, but several authors have reported that the creek downstream of this location typically dried
during periods of low precipitation or warm weather. On December 16, 1987, CDFG surveys
(CDFG 1987) reported that,
“Although there should have been flow from storm runoff, the creek was dry at I-680.”
A survey on March 11, 1992 by HRG (1992) documented a dry channel in Upper Penitencia
Creek,
“…from 150 yards downstream of the Maybury Road crossing to below King Road.”
Since installation of the fish passage and diversion facility at Nobel Avenue in 1999, however,
drying of the channel downstream may occur less frequently than in prior years (J. Abel,
SCVWD, pers. comm., 2006). This is presumably because the diversion is typically only operated
when flow is above about 2.5 cfs, which is the minimum flow necessary for the fishway to
function.
An analysis of the effects of the diversions and water returns on steelhead passage would require
detailed information on the timing and amount of water diverted and discharged to the stream,
and the stream flow and water temperatures during winter and spring periods of adult upstream
migration and juvenile outmigration. Because very little information of this type is available, our
analysis is limited to a largely qualitative evaluation of the potential effects of diversions and
seasonal drying on fish passage.
Available water temperature data, collected by SCVWD at five locations in Upper Penitencia
Creek downstream of Alum Rock Park, are limited to the summers of 2000, 2001, 2002, and 2004
(Figures 4-19 and 4-20). Data from 2001 and 2004, however, only include the later half of the
summer, beginning in late July. Only data from 2000 and 2002, which begin in the month of
May, provide insight into water temperatures during the later portion of the peak steelhead
outmigration period (April–May). These data show that daily average water temperatures in May
downstream of RM 3.7 can range from as low as 55°F to over 70°F (Figures 4-19 and 4-20). This
range includes temperatures that are known to be stressful to outmigrating steelhead. Myrick and
Cech (2001) reported that temperatures >59°F are unsuitable for smolting steelhead, and Zaugg
and Wagner (1973) and Adams et al. (1975), both as cited in ODEQ (1995) found temperatures
>55°F to be stressful (inhibiting gill ATPase activity). McEwan and Jackson (1996) reported that
temperatures <57°F are preferred for steelhead smolt outmigration. This comparison indicates
that water temperatures in the “migration corridor” reach of Upper Penitencia Creek (downstream
of RM 3.5) may be unsuitable for steelhead smolt outmigration by late May. Temperatures
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encountered by smolts earlier in the year, or during periods of higher flows, however, may be low
enough to facilitate successful outmigration. Additional water temperature data, collected in this
reach from March–May, would allow a more conclusive determination of the frequency of water
temperature limitations.
Historical stream flow data for Upper Penitencia Creek are available for the Dorel Dr. gage (SF
83) for the period 1962–2004. This gage, located at RM 3.9, is upstream of the Noble Ave.
diversion and therefore does not reflect alterations to streamflow resulting from downstream
water diversions or returns. Stream flow data from gage SF87, located 1.3 miles (2.1 kilometers)
upstream from the confluence with Coyote Creek at Mabury Avenue, are only available for the
year 2004. Due to the lack of comparative stream flow data, an analysis of the effects of water
diversions is not possible.
The relationship between flow and depth at potential passage barriers and other locations in
Upper Penitencia Creek is largely unexplored, and we know of no analyses of instream flow
requirements for steelhead passage in the creek. Although two critical riffles have been identified
in Upper Penitencia Creek (Table 4-6), no known passage flow has been calculated for these
riffles. For Coyote Creek, the critical passage flow used by FAHCE (2000) was 13 cfs, which is
based on an assumed minimum depth requirement of 0.8 ft (24 cm) for both adult and juvenile
passage. Balance Hydrologics (2002) calculated an average passage discharge of 19 cfs for
critical riffles in Coyote Creek, but no such calculations were made for Upper Penitencia Creek.
While flows downstream of the Dorel gage (RM 3.5) may be sufficient during the winter and
spring spawning and incubation period to allow successful incubation and emergence, juveniles
in this reach are not likely to survive the summer high temperatures and drying of the channel.
Low flows or drying of the stream bed can delay or preclude downstream passage by smolts
during outmigration, and may result in stranding of rearing or outmigrating fish. Because
upstream movement is likely limited by structural impediments and low flows, juveniles in the
drying reach must either attempt to emigrate during their first summer or seek isolated wetted
habitats in which to rear. Juvenile steelhead entering the ocean in their first year (age 0+) have
been shown to have extremely low survival compared to those rearing in fresh water for at least a
year (age 1+ or 2+) (Shapovalov and Taft 1954, Ward et al. 1989). Those that remain in isolated
habitats and temporarily avoid mortality from desiccation, predation, lethal water temperatures, or
other factors may suffer stress related to increased competition, high water temperatures, or
reduced food availability.
Although existing information indicates that stream flow manipulations may have resulted in
slightly increased summer flows in portions of Upper Penitencia Creek relative to historical
conditions, this assessment is based on insufficient flow data to draw positive conclusions. It is
likely, however, that seasonal drying of the lower reaches occurred regularly in Upper Penitencia
Creek under historical conditions. The wet-winter/dry-summer seasonal pattern in central
California results in summer conditions in Upper Penitencia Creek and other local streams that
are warmer and characterized by less flow than “classic” steelhead streams to the north. To some
degree, steelhead in Upper Penitencia Creek would be expected to be adapted to these natural
summer conditions of low flow and warmer water.
Available information indicates that low spring and summer flows and elevated water
temperatures may substantially limit steelhead rearing and outmigration success in Upper
Penitencia Creek. Not enough is known, however, about steelhead life history in the system
(particularly the timing of movement of juveniles), or about flow and temperature patterns, to
understand how channel drying specifically affects steelhead population dynamics. Substantial
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uncertainty also remains regarding the effects of diversions and water returns in the lower portion
of the creek, including the potential tradeoffs between flow augmentation and increased water
temperatures downstream of the percolation ponds. Without additional data it is not possible to
determine the relative importance of each diversion and inflow with regard to steelhead
outmigration success. Additional information on steelhead population ecology (including run
size, outmigration timing, smolt size, food availability, thermal tolerances, and other factors) is
needed to determine the effects of flow-related barriers on steelhead production. Based on
existing information and observations made by other researchers, it is likely that flow-related
barriers, including high water temperatures, can frequently limit steelhead production in Upper
Penitencia Creek.
4.5
O. mykiss Growth
As outlined in our conceptual model for steelhead (Section 3.3), growth of juvenile steelhead
during their freshwater rearing period is believed to be critical to their attaining a size that will
promote survival during outmigration and ocean phases, as well as to the overall viability of the
population. Several studies have shown a strong relationship between the size at which a
steelhead smolt migrates to the ocean and the probability that it returns to freshwater to spawn
(Kabel and German 1967, Hume and Parkinson 1988, Ward and Slaney 1988, Ward et al. 1989).
For example, in a mark-recapture study on the Eel River, Kabel and German (1967) demonstrated
an exponential relationship between smolt size at outmigration and successful adult return. The
increased survival is usually attributed to larger smolts being better able to escape predation
during outmigration, and in the estuary and ocean. Most marine mortality of steelhead occurs
soon after they enter the ocean and predation is believed to be the primary cause of this mortality
(Pearcy 1992).
The most important food source for juvenile salmonids is usually invertebrate drift from riffles.
Benthic macroinvertebrate production is concentrated in highly oxygenated riffle habitats.
Juvenile steelhead can minimize energy expended in feeding by establishing feeding stations
where riffles enter pools or where they can hold near boulders, large wood, or other flow
obstructions while remaining adjacent to higher velocity water with higher food delivery rates.
Invertebrate production in riffles may be reduced by decreased surface flows; changes in channel
geomorphology that reduce available habitat for benthic macroinvertebrates (such as
sedimentation); and poor water quality that may reduce primary and secondary production or
result in direct mortality of invertebrates.
Steelhead summer rearing densities are typically regulated through territorial behavior that
ensures that fish with established territories achieve sufficient growth. In most of the Pacific
Northwest, summer is considered to be the primary growth period for juvenile steelhead
(Barnhart 1991, Dambacher 1991). However, near the southern portion of its range, including
Bay Area streams, the potential for summer growth may be limited if water temperatures are nonlethal but warm enough to increase bioenergetic needs and food supply (i.e., drifting
macroinvertebrates) is limited. This was found to be the case in the nearby Napa River basin
(Stillwater Sciences and Dietrich 2002). When growth rates are low, aggressive interactions with
conspecifics may increase and this may lead to lower juvenile fish densities in areas where
growth potential is low. For example, Suttle et al. (2004) found that aggressive interactions,
including attacks, increased under conditions of low summer growth. This increased aggression
may provide a mechanism for the downstream decline in juvenile steelhead densities observed by
Li (2001) in Upper Penitencia Creek during late summer sampling. Densities of both age 0+ and
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age 1+ steelhead decreased in a downstream direction between RM 5.88 and 3.88 and steelhead
were absent at three sample sites below RM 3.88 (Li 2001). In addition to overall reductions in
fish density, there was a slight shift in preference of age 1+ fish from pool to riffle habitats at
downstream sample sites. Empirical and theoretical evidence suggests that, within reason,
juvenile steelhead can compensate for warm stream temperatures if food availability is high by
moving to habitats with high food delivery in the form of drifting invertebrates (Smith and Li
1983, Smith 1999).
Summer food availability for rearing steelhead in Upper Penitencia Creek and Arroyo Aguague is
unknown. Existing data from Upper Penitencia Creek (USGS 1997, SCVURPPP 2003b) do not
provide a reliable indicator of prey availability for juvenile steelhead because they consist of
benthic samples, and not invertebrate drift. Although benthic data indicate a high diversity and
abundance of the potential drift food source, the delivery (and thus availability) of drifting
invertebrates to fish during the primary summer growth season is highly dependent on surface
flow characteristics. It was not possible as part of this study to evaluate summer flow patterns,
summer invertebrate drift, or the availability of suitable feeding stations in the primary rearing
reach during the summer low flow period.
Water temperature is a particularly relevant parameter for understanding constraints on steelhead
because steelhead rear as juveniles in freshwater for one or more years. Steelhead may experience
several summer seasons while rearing, during which they may be subject to warm water
temperatures and the resulting thermal stresses. The direct impacts of high temperatures may
include both acute and chronic effects. Acute effects tend to involve decreased or disrupted
enzyme function, which may compromise a wide range of physiological functions and result in
total incapacitation and death. Chronic effects involve physiological changes that slowly degrade
the condition of the fish, such as increased metabolic rate (which reduces growth efficiency),
reduced immune system function (which increases susceptibility to disease), or an increased
tendency to become exhausted (which reduces foraging efficiency). Indirectly, high temperatures
may affect coldwater fish such as steelhead by reducing dissolved oxygen (the dissolved oxygen
capacity of water is inversely related to temperature), or by changing the behavior or physiology
that affect the competitive balance among species and hence may result in a shift in fish species
composition or relative abundance. In addition, because steelhead are sensitive to increases in
temperature, any additional factors that might increase physiological stress, such as disease, food
limitations, elevated turbidity, or increased competition between species, have the potential to
compound the impact of elevated temperatures.
Because the timing of this project precluded us from collecting summer stream temperature data,
we characterized existing temperature patterns in Upper Penitencia Creek using information
collected by the SCVWD. Stream temperatures measured during summer and fall of 2000, 2001,
2002, and 2004 at five sites between RM 3.7 and the mouth of Upper Penitencia Creek (Table 48) were obtained from SCVWD. The uppermost of these sites is close to the lowermost extent of
juvenile rearing in Upper Penitencia Creek (Li 2001; see also Section 4.1), and therefore, thermal
conditions in the majority (and presumably most suitable) of rearing habitat is unknown. We
found that maximum summer water temperatures at the uppermost monitoring site (RM 3.7)
exceeded lethal limits reported for steelhead and rainbow trout (75–80°F; Hokanson et al. 1977,
Bell 1991, Bjornn and Reiser 1991, Myrick and Cech 2001), but we do not know if temperatures
at this site are representative of upstream conditions. In general, as stream gradient, elevation, and
streamflow decrease, and solar insolation increases, stream temperatures increase. Therefore, the
upper reaches of Upper Penitencia Creek are expected to have lower stream temperatures,
although their true thermal regime is unknown.
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Table 4-8. Location of Upper Penitencia Creek temperature data loggers.
Miles upstream
of Coyote Creek
Location Description
0.1
Near Coyote Creek confluence
1.2
Education Park Drive
1.3
Mabury Road
3.3
Percolation Ponds
3.7
Noble Avenue
It is likely that the summer season is a period of low growth for steelhead in Upper Penitencia
Creek due to low stream flows and warm temperatures. Very low summer growth and even
negative growth (weight loss) by juvenile steelhead has been documented in Napa River
tributaries with very low summer stream flows and high water temperatures (Stillwater Sciences
and Dietrich 2002). In Upper Penitencia Creek there is little available information specific to the
area of stream upstream of RM 3.7, where most of the rearing habitat is found. However, indirect
evidence suggests that growth potential may be suboptimal in Upper Penitencia Creek during
some years. Lengths of steelhead smolts captured in Coyote Creek trap in 1999 (FAHCE 2000)
indicate that smolt lengths are unimodal with peaks within a range that is typical of steelhead
populations in other portions of the species’ range (e.g., 160–180 mm) (Figure 4-5). However,
smolt lengths in the year 2000 are shifted toward smaller lengths with the majority of smolts
falling below lengths (e.g., 160 mm) that other studies (e.g., Kabel and German 1967) have
shown are related to poor ocean survival. Whether these differences in length frequencies reflect
annual differences in growth opportunity or are a byproduct of an incomplete sampling of the
smolt outmigration period is unknown. Additionally, it is not known what portion of the smolts
captured at the Coyote Creek trap originated in Upper Penitencia Creek, nor is their length
frequency known.
Naturally low flows and high summer water temperatures may result in low summer steelhead
growth rates in Upper Penitencia Creek (see Appendix A-7 for available water temperature data).
However, the resulting late summer/early fall population of age 1+ steelhead is still high relative
to the winter carrying capacity, indicating that summer conditions do not currently limit the
steelhead population in Upper Penitencia Creek. Although results from our 2005 fall snorkel
survey may have been influenced by the particularly wet spring and early summer conditions
providing increased streamflow, they are similar to a previous late-summer juvenile estimate that
occurred during a year (2000) where observed summer stream temperatures reached near-lethal
levels at the uppermost temperature monitoring site at stream mile 3.7 (Figure 4-19).
In summary, there is some uncertainty related to summer rearing conditions for steelhead within
the watershed, particularly with regard to steelhead growth potential. The available information
indicates that summer rearing habitat does not currently limit steelhead population growth. Our
modeling results suggest that increases in winter habitat quality for age 1+ steelhead would lead
to large benefits in smolt production. However, with improvements to winter habitat conditions,
other factors, particularly summer rearing conditions for age 1+ steelhead, may become more
important as limitations to additional population growth. Confidence in these model results
would be greatly improved by additional seasonal monitoring of seasonal steelhead abundance.
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5
LIMITING FACTORS SYNTHESIS
In conducting the limiting factors analysis we attempted to: (1) systematically review steelhead
life history requirements, (2) identify the full range of potential factors that might be operating to
limit the steelhead population in Upper Penitencia Creek, (3) screen these potential limiting
factors using available information and initial reconnaissance observations on current watershed
conditions to develop hypotheses about those factors thought to be of greatest likely importance
in the basin, and (4) test and refine hypotheses using the focused studies described above. Time
and funding constraints for this project, however, limited our ability to address some key
uncertainties about potential limiting factors. Because of limitations in our understanding of
current conditions and how limiting factors have operated in the basin, there are varying degrees
of uncertainty associated with our identification and ranking of key limiting factors. Future
studies, including collection of additional data on steelhead habitat use and carrying capacity in
Upper Penitencia Creek for use in supplemental population modeling, have been proposed in
Section 7 to address what we feel are the most important uncertainties related to management of
aquatic resources in the watershed. A synthesis of the conceptual models, hypotheses, and
findings developed during this study is provided below.
Review of available information and analysis of limiting factors for steelhead in Upper Penitencia
Creek indicates that, despite human land use and water use activities in the watershed, alterations
to the creek have not seriously compromised the potential of the system to support a viable run of
steelhead. Although the urbanized areas of the watershed, which have received the most intense
human use, did not likely support spawning and rearing of steelhead historically due to
intermittent stream flow and warm temperatures, they continue to serve as a migratory corridor
for adult upstream migration and downstream migration of smolts from the upper watershed. The
primary hypothesized impact to steelhead in Upper Penitencia Creek has been a general
simplification of the channel, resulting in somewhat reduced quantity and quality of habitat for
spawning and rearing life stages. Due to the lack of data describing the pre-disturbance (i.e.,
reference) conditions in the watershed, however, this hypothesis remains largely unverified.
Currently, the Upper Penitencia Creek watershed supports juvenile steelhead in the area from
approximately 3.5 miles (5.6 kilometers) upstream of the confluence with Coyote Creek upstream
to waterfall barriers in Upper Penitencia Creek and Arroyo Aguague. Results from an extensive
snorkel sampling effort during spring and fall 2005 indicated that the watershed supported
between 1,300 and 1,500 age 1+ and older steelhead, of which age 2+ and older fish comprised
approximately 5 to 10 %. To help synthesize the information collected on steelhead habitat
conditions and juvenile abundance in Upper Penitencia Creek, we conducted a population
dynamics modeling exercise based on fish and habitat data collected during this and previous
studies (Appendix A-2).
Our gravel permeability study indicates that spawning gravels in Upper Penitencia Creek and
Arroyo Aguague have low to moderate permeability, probably due to fine sediment intrusion.
Although the survival of steelhead eggs and larvae is likely reduced by low permeability of
spawning gravels, our analysis demonstrates that this factor is not sufficient to cause a decline in
steelhead population levels. The quantity and quality of spawning gravel in relatively unaltered
portions of the channel—primarily the upstream reaches of Upper Penitencia Creek and Arroyo
Aguague below the natural waterfalls—likely provide spawning and incubation conditions
sufficient to fully seed the available rearing habitat. Population modeling suggests that under
current conditions we would not expect significant changes in smolt production even if egg-toemergence survival was increased by improving spawning gravel quality. Similarly, the quantity
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53
of spawning gravel in the primary rearing reach (upstream of RM 3.5), although limited in area
and distribution, is not likely limiting the steelhead population.
Results from our fish passage analysis indicate that artificial structural barriers are not likely to
restrict access by adult steelhead to habitat in upstream reaches. Flow-related passage restrictions
may, however, compromise habitat connectivity and reduce successful outmigration opportunities
during late spring. Although flow augmentation and diversions affect the majority of the creek
and drying of the channel in downstream reaches has been documented to reduce passage
opportunities for outmigrating steelhead smolts in some years (e.g., SCBWMI 2003, Smith 1998),
it remains unclear whether this phenomenon is exacerbated by anthropogenic activities. It is
likely that seasonal drying of the lower reaches occurred regularly in Upper Penitencia Creek
under historical conditions due to the warm, dry climate and highly permeable alluvial materials
present in the Santa Clara Valley. Periodic flow augmentation downstream of Cherry Flat Dam is
believed to have increased the extent and duration of wetted habitat in Alum Rock Park during
summer, but the exact amount of habitat gained and the effects of this increase on steelhead
production are unknown. In addition to low flows, high water temperatures in the migration
corridor reach (downstream of RM 3.5) may also limit the ability of steelhead smolts to migrate
to the bay, especially if they occur during the April-May outmigration peak. Low flows may also
render some artificial structures impassible to outmigrating smolts but the timing, frequency, or
severity of this occurrence could not be documented using available information. If low flows and
resulting high water temperatures actually prevent smolt outmigration, reduced steelhead
production can be expected.
Our analysis of winter rearing habitat suggests that highly embedded cobble and boulder
substrates may limit the winter carrying capacity of the Upper Penitencia Creek watershed.
Although the abundance of cobble and boulder substrates in the primary rearing reach is
relatively high, intrusion of sediment into interstitial spaces reduces the area available for juvenile
steelhead concealment and velocity refuge during high winter flows. Further, the artificial
straightening of the channel and hardening of the banks at multiple locations in Alum Rock Park
have in places resulted in a steep-sided, box-like channel in which increased water velocity
during high winter flows may severely reduce the overwintering success of juvenile steelhead.
Despite observations that sediment ranging in size from silt to small gravel is causing
embeddedness of coarser substrates and reducing interstitial space, based on best professional
judgment the existing evidence was not sufficient to determine whether a significant fraction of
the sediment load in Upper Penitencia Creek is derived from anthropogenic sources. The
naturally erosive underlying geology and steep topography present in much of the upper basin,
together with local seismic activity and the intense, episodic winter rainfall characteristic of
California’s Mediterranean climate, combine to produce a naturally high sediment load in Upper
Penitencia Creek. Additional analyses of sediment sources and relative contributions would be
necessary to reach a more definitive conclusion regarding anthropogenic sediment inputs.
While available information suggests that summer habitat does not limit the steelhead population
in Upper Penitencia Creek because of winter habitat limitations for age 0+ and 1+ fish, there is a
great deal of uncertainty related to summer rearing conditions within the watershed. Available
data were collected from limited and sporadic monitoring, making annual trends and variability in
stream conditions and population response difficult to characterize. Although population
modeling indicates that winter rearing habitat is currently more limiting than summer habitat,
summer rearing success may be limited by flow-related reductions in food delivery and increases
in water temperature, especially during critically dry years. Additional studies to characterize
summer growth and document late summer steelhead densities during additional years would
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54
greatly reduce uncertainties and improve our ability to identify the underlying causes of
population limitations.
The lack of detailed historical information on fish populations and habitat conditions and the
extensive period of human use in the Upper Penitencia Creek watershed make it difficult to
identify pre-disturbance conditions. Studies of historical ecology of several local watersheds,
including Upper Penitencia Creek, are currently being conducted by the San Francisco Estuary
Institute. Only limited information on the historical conditions in the Upper Penitencia Creek
watershed, however, were available to us during our analysis. Nevertheless, we have used
currently available information to analyze the current habitat conditions within the watershed in
relation to likely historical conditions. Our current hypotheses regarding changes from historical
conditions and their likely effects on various life stages of steelhead are summarized in Table 5-1.
Table 5-1. Summary of conceptual models and hypotheses regarding historical and current
conditions in the Upper Penitencia Creek watershed and their potential effects on different life
stages of steelhead.
Life History
Stage
Upstream
migration
Hypothesized Historical Condition
Current Condition
Steelhead accessed Upper Penitencia
Creek each year after the onset of winter
rains that facilitated passage through
seasonally dry reaches.
Flow regulation in Upper Penitencia
Creek is generally restricted to summer
months, and thus has little effect on
upstream fish passage.
Natural hydrologic fluctuation delayed
steelhead passage during dry years but,
besides low flow, there were probably no
significant in-channel barriers or
impediments to upstream migration of
adults.
Despite rapid and widespread urban
development in the lower portion of the
watershed, the majority of the drainage
area remains relatively undeveloped. The
duration and frequency of winter high
flow events remains similar to historical
conditions.
The natural waterfalls in Upper Penitencia
Creek and Arroyo Aguague were the
upstream limits of anadromous fish
access.
LWD formed deep pools, providing
holding habitat for anadromous adults.
Although numerous weirs, grade control
structures, and other structures have been
built in the channel, upstream passage by
steelhead remains relatively unimpeded
up to the natural waterfalls.
Reductions in LWD may have resulted in
fewer deep pools, reduced holding habitat
for spawners and reduced spawning
gravel storage.
Spawning
and
incubation
Spawning gravel was relatively abundant
in the primary rearing reach, but gravel
quality may have been reduced by
naturally high fine sediment loads
originating from the steep, erosive upper
watershed.
Localized bed mobility may have
occurred at high flows, especially in areas
where steep, narrow canyon walls or
bedrock outcrops concentrated stream
flow. Redd scour was probably rare,
however, because suitable quantities of
spawning gravel were not likely to occur
Spawning habitat quality in the primary
rearing reach is relatively low, as
evidenced by low to moderate
permeability. This likely results in
reduced survival of steelhead eggs and
alevins (larvae). Spawning habitat,
however, is believed to be sufficient to
fully seed rearing habitat under current
conditions.
The quantity and quality of spawning
gravel in relatively unaltered portions of
the channel—primarily the upstream
reaches of Upper Penitencia Creek and
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55
Life History
Stage
in areas with extremely high bed mobility.
Arroyo Aguague below the natural
waterfalls—likely provide spawning and
incubation conditions sufficient to fully
seed the available rearing habitat.
Juvenile rearing was limited to upstream
perennial reaches that were well shaded
with riparian forest and had suitably cool
stream temperatures.
Juvenile rearing continues to be restricted
to upstream perennial reaches, with
summer flow augmentation from Cherry
Flat reservoir maintaining a wetted
channel downstream as far as the
urbanized reach.
Lower reaches of Upper Penitencia Creek
likely did not have surface flow during
summer and early fall months of most
years.
Pools with complex structural habitat and
relatively cool water likely provided the
primary summer rearing habitat in Upper
Well developed native riparian forests in
the upper watershed probably provided
moderate to high amounts of LWD,
leading to frequent pool development.
Juvenile
rearing
Current Condition
The coarse streambed in the upper
watershed likely provided a high amount
of potentially suitable overwintering
habitat. Natural sediment may have
chronically reduced overwintering habitat
quality (but actual quality is unknown).
Flows were probably lower and
temperatures higher than more northerly
steelhead streams, but the local steelhead
race was probably at least partially
adapted to cope with these conditions.
At low flows, numerous instream
structures may limit the ability of juvenile
fish to move from seasonally dry habitats
to perennial habitat. Perennial habitat,
however, may already be at carrying
capacity, in which case restricted
movement by juveniles would result in no
net decrease in smolt production.
The quality of rearing habitat available is
diminished due to channel alterations,
which have reduced summer habitat by
reducing channel complexity and habitat
diversity, and reduced winter habitat by
increasing water velocity during storm
events.
Sediment deposition is reducing the
availability of interstitial space in coarse
substrates used by overwintering
steelhead, but the degree to which
smaller-grained sediment (small gravel,
sand, and finer) inputs may exceed natural
background levels remains unclear.
The stream channel likely has fewer pools
and pool quality is reduced due to incision
and reduction in LWD levels. Artificial
bank hardening and channel modification
in Alum Rock Park and at several
downstream locations has contributed to
channel incision and reduced channel
migration. Disconnection of the stream
from its historical floodplain has in places
reduced the input of organic matter to the
stream channel and reduced secondary
winter refuge habitat.
Outmigration
During wet years smolt outmigration
occurred over a wide time period from
late winter to early summer, with the peak
likely occurring in April and May. During
dry years, interruption of smolt
outmigration likely occurred when
Water diversion may cause early drying
of downstream reaches. Outmigration
may be interrupted more frequently,
possibly resulting in substantially reduced
smolt outmigration success. Due to a lack
of specific information describing
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56
Life History
Stage
downstream reaches of Upper Penitencia
Creek dried during the spring.
Current Condition
diversion and water return operations, as
well as limited stream hydrology data for
these reaches, considerable uncertainty
remains regarding the effects of these
operations on downstream smolt passage.
Return flows may periodically augment
streamflow in downstream reaches—
primarily from April–October—but warm
imported water reduces suitability for
outmigrating smolts. Available
information is insufficient, however, to
determine the relative importance of any
specific diversion or flow return on
steelhead smolt success.
Summary of
steelhead
production
potential
Steelhead production in Upper Penitencia
Creek would have been lower than in
larger drainages in the Santa Clara Basin,
but perennial flow in the upper reaches
and relatively high quality habitat would
have supported production levels fairly
typical for a stream of its size. Compared
with basins having lower natural sediment
production, however, steelhead
production in Upper Penitencia Creek
may have been somewhat reduced due
primarily to lower quality overwintering
habitat.
Production would have been limited
occasionally during drought years, but the
availability of suitable spawning and
rearing habitat in the upper reaches would
have spread risks and reduced the odds of
substantial year-class failures.
Steelhead production may be somewhat
reduced from hypothesized historical
levels, which would be primarily
attributable to habitat simplification,
periodic reduction of outmigration
passage opportunities, reduced pool
quality, and possibly increased
sedimentation of overwintering habitat.
Reduced success of outmigrating
steelhead smolts may result in the return
of low numbers of anadromous adults in
some years.
Overall habitat quality is somewhat
diminished due to altered channel
morphology, including increased water
velocity in modified reaches during storm
events, reduced channel complexity, and
reduced habitat diversity.
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6
CONCLUSIONS AND PROPOSED ACTIONS
The limiting factors analysis was based on the best available existing information and the results
from each of the focused studies. Consistent with the limiting factors approach, key findings are
summarized by steelhead life stage in Table 6-1. For each life stage we have described important
information needs that were identified based on currently available information and hypotheses
and these needs are presented as recommended future studies. Recommended monitoring and
management actions that are not explicitly linked to the requirements of a specific steelhead life
stage are listed separately at the end of this section.
The recommendations for additional studies presented below may be implemented as individual
studies or integrated with existing and/or proposed programs. We expect that local knowledge
and experience, conveyed through input from local landowners, resource managers, and
stakeholders, will enhance and bring specificity to the recommendations provided herein prior to
implementation. The results of this study and future studies, including those currently underway
or planned, should be used to develop a better understanding of priorities for the Upper Penitencia
Creek watershed and to place in context the management priorities for Upper Penitencia Creek
relative to other streams and rivers in the Santa Clara Valley as a whole.
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Table 6-1. Summary of conclusions and recommended studies.
Juvenile
rearing
Spawning and incubation
Upstream migration
Life
history
stage
Conclusion
Although numerous weirs, grade control
structures, and other structures have been built in
the channel, upstream passage by steelhead
remains relatively unimpeded up to the natural
waterfalls. Nevertheless, the grade control
structure at the Youth Science Institute has the
potential to reduce upstream passage opportunities
at some flow levels.
Results of gravel permeability and other analyses
strongly suggest that steelhead production is not
limited by spawning habitat quality or quantity in
Upper Penitencia Creek. Predicted survival of
steelhead eggs and alevins is relatively low, due to
low-moderate permeability of spawning gravels.
The degree to which this is attributable to
anthropogenic disturbance or the naturally high
sediment load in the Upper Penitencia Creek
watershed is unknown. Under existing conditions,
improved spawning gravel permeability and
increased egg-to-emergence survival would not be
expected to increase smolt production because of
population limitations at other life stages.
Summer Rearing: The degree to which summer
rearing limits the production of steelhead is
uncertain. Summer rearing habitat does not appear
to be substantially impacted by fine sediment in
pools. Potential limitations to steelhead density
and fish growth from low streamflow and high
water temperatures were identified. Preliminary
Potential studies to reduce
uncertainties
Conduct a detailed analysis to
determine the timing and
magnitude of flows necessary
for upstream passage by adults.
This is especially important at
the YSI grade control structure
and the two previouslyidentified critical riffles in the
“migration corridor” reach.
None recommended (but see
Recommended Management
Actions at the end of Section
6).
Monitor juvenile steelhead
populations in established
sample reaches twice annually
(fall and spring) to collect
habitat-specific population data
and determine summer (and
winter) carrying capacity.
One-time
or ongoing
study?
Potential
importance to
steelhead
population
dynamics
Current
relative
uncertainty
Potential
reduction in
uncertainty
Relative
priority
ranking
One-time
Moderate
Moderate
High
8
NA
NA
NA
NA
Ongoing
Moderate
High
Moderate–
High
4
(same
study as
for winter
rearing)
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Life
history
stage
Conclusion
modeling suggests that summer carrying capacity
is higher than winter carrying capacity for age 1+
steelhead but this conclusion should be considered
preliminary until further studies are conducted.
uncertainties
Monitor stream temperatures
year-round at multiple
locations in Upper Penitencia
Creek for several years to
improve our understanding of
seasonal and annual variability
in stream temperatures that
might adversely affect
steelhead and other aquatic
organisms. The need for stream
temperature data is especially
critical in Alum Rock Park,
where most rearing likely takes
place.
Conduct seasonal fish growth
studies over the course of a full
year to determine whether
summer growth is limited by
water temperatures, food, and
flow, and whether potential
low or negative summer
growth can be offset by growth
during the spring and fall.
One-time
or ongoing
study?
Potential
importance to
steelhead
population
dynamics
Current
relative
uncertainty
Potential
reduction in
uncertainty
Relative
priority
ranking
Ongoing
High
High
High
5
One-time
(full year)
Moderate
Moderate
High
7
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Life
history
stage
Conclusion
Winter Rearing- High levels of coarse substrate
embeddedness are believed to result in low winter
carrying capacity for juvenile steelhead.
Preliminary modeling suggests that an increase in
the quantity or quality of winter refuge habitat
would likely increase smolt production.
Additional studies are needed to quantify the type
and quality of available overwintering habitat
throughout the primary rearing reach and the
mechanisms responsible for the high levels of
embeddedness.
uncertainties
Additional population surveys
in spring 2006 would provide
the data necessary to document
winter survival and carrying
capacity. Spring densities of
age 1+ or greater steelhead
obtained from snorkel surveys
in the same habitat units
snorkeled in 2005 would
greatly aid in determining
whether winter rearing habitat
is limiting smolt production in
Upper Penitencia Creek. If
conducted in conjunction with
recommended fall population
monitoring (see Summer
Rearing above), this
information would greatly aid
in determining the relative
importance of winter habitat as
a limiting factor for steelhead.
Monitor juvenile steelhead
populations in established
sample reaches twice annually
(fall and spring) to collect
habitat-specific population data
and determine winter (and
summer) carrying capacity.
One-time
or ongoing
study?
Potential
importance to
steelhead
population
dynamics
Current
relative
uncertainty
Potential
reduction in
uncertainty
Relative
priority
ranking
One-time
High
High
High
3
Moderate–
High
4
(same
study as
for
summer
rearing)
Ongoing
Moderate
High
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Outmigration
Life
history
stage
Conclusion
Steelhead outmigration success is likely limited
by seasonal drying of the channel, and this impact
can be exacerbated when habitat connectivity is
interrupted by flow diversion. At very low flows,
otherwise passable artificial structures may
become impediments to downstream smolt
passage. Although seasonal drying is most likely a
natural phenomenon in Upper Penitencia Creek,
we believe it to be a potential limiting factor of
current importance. Available data were not
sufficient to determine the extent to which the
frequency of channel drying during outmigration
has changed relative to historical conditions, or
which diversion(s) have the most pronounced
effect on downstream flow and water temperature.
uncertainties
Collect detailed habitat data to
document the location and
carrying capacity of critical
steelhead habitat, including the
extent of suitable winter habitat
(e.g., unembedded cobble and
boulder substrate, large woody
debris jams, root wads, offchannel habitat) in the primary
rearing reach in Upper
Penitencia Creek and Arroyo
Aguague.
Conduct annual smolt trapping
in Upper Penitencia Creek
during the spring outmigration
period (March–June) to
determine smolt size,
abundance, and outmigration
timing.
Conduct a detailed analysis to
determine the timing and
magnitude of flows necessary
for downstream passage by
smolts. This study has been
identified as “ongoing” due to
the need to collect data under a
variety of flow conditions.
One-time
or ongoing
study?
Potential
importance to
steelhead
population
dynamics
Current
relative
uncertainty
Potential
reduction in
uncertainty
Relative
priority
ranking
One-time
Moderate
Moderate
Moderate
6
Ongoing
High
High
High
1
Ongoing
High
High
High
2
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In addition to the key findings and recommended studies listed in Table 6-1, we have identified
the following recommended monitoring and management actions that are not linked to a specific
steelhead life stage. We believe the monitoring recommendations listed below would help fill
data gaps and potentially provide significant contributions to the understanding of both physical
and biological processes in the Upper Penitencia Creek watershed.
Recommended Monitoring
•
Install and monitor a stream flow gage in Alum Rock Park to provide data on seasonal
flow patterns.
•
Continued stream flow monitoring at gage SF 87, at Mabury Avenue, is recommended.
Because the effects of seasonal stream drying are dependent on the magnitude and timing
of flows, especially in the lower reaches of the creek that are subject to diversion and
flow augmentation, additional streamflow monitoring data are needed downstream of the
Noble Avenue diversion to determine the impacts of flow-related barriers on steelhead
production.
Recommended management actions listed below are likewise not specifically linked to a
particular steelhead life stage, but are considered to be important actions with the potential to
benefit steelhead and other aquatic organisms and uses in the Upper Penitencia Creek watershed.
Recommended Management Actions
•
Develop a biologically- and hydrologically-based operation schedule for water releases
from Cherry Flat Reservoir. In conjunction with stream flow monitoring in Alum Rock
Park (see recommendation below), a formalized operations schedule would enable
adaptive flow management in the primary rearing reach of Upper Penitencia Creek.
•
Develop and implement fine sediment reduction measures in the upper watershed,
especially in the Upper Penitencia Creek and Arroyo Aguague drainages upstream of
their confluence. A pilot-level sediment source analysis focusing on potential sediment
input from roads and grazing in Upper Penitencia Creek and Arroyo Aguague would help
identify sediment management priorities. As a first step in characterizing anthropogenic
fine sediment contributions, this analysis could be conducted using existing data sources,
such as SCVWD GIS data, aerial photographs, and limited field reconnaissance.
•
Remove or modify the concrete grade control weir at the Youth Science Institute in Alum
Rock Park to reduce the potential for upstream passage limitations by adult steelhead.
The importance of removing this structure could be largely determined by a detailed
passage flow analysis, as recommended in Table 6-1 for the Upstream Migration life
stage. In addition, an opportunity exists to re-engineer this structure for use as a steelhead
counting weir. This would provide valuable information on the abundance and timing of
steelhead spawners in the creek and provide an educational opportunity for the Youth
Science Institute.
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7
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FIGURES
Stillwater Sciences
80
5
4.5
70
4
3.5
50
3
40
2.5
2
30
1.5
20
1
Mt Hamilton Temperature
San Jose Temperature
Mt Hamilton Precipitation
San Jose Precipitation
10
0.5
0
0
J
F
M
A
M
J
J
A
S
O
N
D
Month
Figure 2-1. Monthly mean temperature and precipitation in Mount Hamilton, CA, and San Jose, CA,
average from 1948-2004.
Average Precipitation (inches)
Monthly Mean Temperature (F)
60
550
500
450
Mean Daily Streamflow (cfs)
400
350
300
250
200
150
100
50
ct
-0
5
O
ct
-0
1
O
ct
-9
7
O
ct
-9
3
O
ct
-8
9
O
ct
-8
5
O
ct
-8
1
O
ct
-7
7
O
ct
-7
3
O
ct
-6
9
O
ct
-6
5
O
O
ct
-6
1
0
Water Year
Figure 2-2. Mean daily streamflow in Upper Penitencia Creek at SCVWD gage SF 83 at Dorel Drive, Water
Years 1962-2004.
d
N Jackson
Capitol Ave
Ave
N King R
1939
Capitol Ave
N
N Kin
Jackson
g Rd
Ave
Mabury
Rd
Mabury
Rd
Mabury
Rd
Capitol Ave
I-680
N Jackson
N Kin
g Rd
Ave
1960
2004
Figure 2-3. Upper Penitencia Creek land use comparison between years 1939,
1960, and 2004 (Scale 1 inch= 0.195 miles). Note that stream channel is shown for
comparative purposes, and is not a GIS layer.
Figure 3-1. Natural fish passage barriers: waterfalls in Arroyo Aguague (left) and Upper Penitencia Creek
(right).
Factors Affecting Upstream Migration
•Attraction flows
•Physical migration barriers
•Environmental migration barriers
•Migration corridor hazards
Upper P
enit
enc
ia
SPAWNING
Cr
ee
k
s
Re
out
t Tr
en
id
UPSTREAM
MIGRATION
INCUBATION
y
ar
tu
Es
Factors Affecting Estuary
and Ocean Rearing
•Loss of estuarine rearing
habitat
•Water quality and
temperature
•Harvest
•Ocean conditions
•Predation
Factors Affecting Spawning and
Incubation
•Spawning gravel quantity and redd
superimposition
•Spawning gravel quality
•Water quality and temperature
•Substrate mobility/scouring
•Redd dewatering
ESTUARY and
OCEAN
REARING
&
O
ce
an
Factors Affecting Outmigration
•Adequate flows for outmigration
•Predation
•Diversion hazards
REARING
OUTMIGRATION
(steelhead only)
Factors Affecting Juvenile
Rearing
•Availability of summer rearing
habitat
•Availability of overwintering
habitat
•Stranding by low flows
•Displacement by high flows
•Predation
•Food availability
•Interspecific interactions between
native species
•Competition with introduced
species
Figure 3-2. Steelhead and resident rainbow trout life cycle and potential factors thought to affect the
abundance of various life stages.
0.35
pool units
Spring 2005
Fall 2005
Fish Density (fish/ft²)
0.30
0.25
0.20
0.15
0.10
0.05
398
400
407
423
425
452
464
467
482
483
498
507
519
525
536
541
559
561
574
588
593
611
617
630
633
640
656
660
669
685
689
700
702
712
725
726
727
739
740
752
753
758
761
762
763
765
774
784
786
791
800
807
810
2
4
6
7
9
12
16
18
21
26
27
28
33
35
0.00
lower reach
upper reach
arroyo aguaque
Habitat Unit
Figure 4-1. Spring and Fall 2005 densities of age 0+ O. mykiss in pools (shaded) and runs in Upper
0.050
0.045
pool units
Spring 2005
Fall 2005
Fish Density (fish/ft²)
0.040
0.035
0.030
0.025
0.020
0.015
0.010
0.005
398
400
407
423
425
452
464
467
482
483
498
507
519
525
536
541
559
561
574
588
593
611
617
630
633
640
656
660
669
685
689
700
702
712
725
726
727
739
740
752
753
758
761
762
763
765
774
784
786
791
800
807
810
2
4
6
7
9
12
16
18
21
26
27
28
33
35
0.000
lower reach
upper reach
arroyo aguaque
Habitat Unit
Figure 4-2. Spring and Fall 2005 densities of age 1 and older O. mykiss in pools (shaded) and runs in
Upper Penitencia Creek and Arroyo Aguague.
3500
Spring 2005 estimates
Fall 2005 estimates
3000
Population Estimates
2500
2000
1500
1000
500
0
pools
runs
lower
total
pools
runs
upper
total
pools
runs
total
arroyo
Figure 4-3. Spring and Fall 2005 population estimates and 95% confidence intervals for age 0+ O. mykiss
in lower and upper reaches of Upper Penitencia Creek and in Arroyo Aguague.
700
Spring 2005 estimates
Fall 2005 estimates
600
Population Estimates
500
400
300
200
100
0
pools
runs
lower
total
pools
runs
upper
total
pools
runs
total
arroyo
Figure 4-4. Spring and Fall 2005 population estimates and 95% confidence intervals for age 1 and older O.
mykiss in lower and upper reaches of Upper Penitencia Creek and in Arroyo Aguague.
(
)
pp
35
(
)
35
A
B
Source: Smith (1997)
30
Source: SCVWD outmigrant trapping data
30
n=111
n=15
20
20
Number
25
Number
25
15
15
10
10
5
5
0
0
0
60
120
180
240
300
360
420
0
60
120
180
Standard Length (mm)
240
300
360
420
pp
(
)
pp
35
(
)
35
C
D
30
30
n=239
n=158
25
20
20
Number
Number
25
15
15
10
10
5
5
0
0
0
60
120
180
240
300
360
420
0
60
120
180
240
300
360
Figure 4-5. Length frequency histograms for steelhead in Upper Penitencia Creek in 1997 (A), and from
outmigrant traps in Coyote Creek during 1998 (B), 1999 (C), and 2000 (D).
420
Capitol
Ave
Coyote
ssa Rd
Berrye
ot
Coy
ssa Rd
Berrye
eek
e Cr
1951
Ave
Capitol
Ave
Creek
1899
Capitol
te
yo Creek
Co
1873
Figure 4-6. Upper Penitencia Creek stream channel comparison between
years 1873, 1899, and 1951 (Scale 1 inch= 0.663 miles). Historical maps
courtesy of San Francisco Estuary Institute, Historical Ecology Program.
100%
90%
80%
McCuddin 1977 (chinook)
Tagart 1976 (coho)
Fitted model
90% confidence limits
95% confidence limits
Survival-to-Emergence
70%
60%
50%
40%
30%
20%
Survival = -0.825 + 0.149 Ln Permeability
10%
Adjusted R2 = 0.85
p < 10-7
0%
100
1,000
10,000
100,000
Permeability (cm/hr)
Figure 4-7. The egg survival-to-emergence index used to interpret the relative impact of measured
permeability on steelhead production is based on the regression derived from data collected by Tagart
(1976) for coho salmon and McCuddin (1977) for Chinook salmon.
1.0
0.9
Fraction of maximum smolt production
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
Survival-to-emergence
Figure 4-8. Expected potential smolt production as a function of emergence survival.
0.8
0.9
1
2000
Spawning Gravel area
Reach Boundaries
1750
Spawning gravel area (ft²)
1500
1250
UUP
ARP
URB
1000
AAG
750
500
250
7.
5
7
6.
5
6
5.
5
5
4.
5
4
3.
5
3
2.
5
2
1.
5
1
0.
5
0
0
River Mile
Figure 4-9. Area (ft²) of spawning gravel, summed over 0.1 mi increments upstream from the mouth of
Upper Penitencia Creek (includes both Upper Penitencia Creek and Arroyo Aguague data).
1.0
predicted survival to emergence
0.9
Reach boundaries
Predicted survival to emergence
0.8
0.7
0.6
0.5
0.4
0.3
0.2
UUP
0.1
URB
ARP
AAG
7.
5
7
6.
5
6
5.
5
5
4.
5
4
3.
5
3
2.
5
2
0.0
River Mile
Figure 4-10. Predicted survival to emergence at permeability sites in Upper Penitencia Creek and Arroyo
Aguague.
1.0
Reach boundaries
0.9
Predicted survival to emergence
0.8
0.7
0.6
0.5
ARP2
URB2
ARP1
0.4
ARP3
URB1
AAG
UUP2
0.3
0.2
UUP
0.1
URB
AAG
ARP
River mile
Figure 4-11. Predicted median survival to emergence, with 95% confidence intervals, for sampled
reaches in Upper Penitencia Creek and Arroyo Aguague.
7.
5
7.
0
6.
5
6.
0
5.
5
5.
0
4.
5
4.
0
3.
5
3.
0
2.
5
2.
0
0.0
25
UUP
HIGH
URB
ARP
AAG
20
MODERATE
% pool filled
15
10
LOW
5
% pool filled
Reach boundaries
River Mile
Figure 4-12. Pool filling in Upper Penitencia Creek and Arroyo Aguague. Values < 10% should be
interpreted as low in basins with fines-rich parent material, values of 10-20% are moderate, and > 20%
are high (Lisle and Hilton 1999, Kondolf et al. 2003).
7.
5
7.
0
6.
5
6.
0
5.
5
5.
0
4.
5
4.
0
3.
5
3.
0
2.
5
2.
0
0
25
UUP
URB
ARP
AAG
20
% pool filled
15
ARP2
10
URB1
UUP2
5
AAG
ARP1
ARP3
Reach boundary
River mile
Figure 4-13. Median V-star (pool filling) values, with 95% confidence intervals, for sampled reaches in
Upper Penitencia Creek and Arroyo Aguague.
7.
5
7.
0
6.
5
6.
0
5.
5
5.
0
4.
5
4.
0
3.
5
3.
0
2.
5
2.
0
0
100%
Boulder
90%
Cobble
80%
70%
Percent (%)
60%
50%
40%
30%
20%
10%
7.
0
6.
5
6.
0
5.
5
5.
0
4.
5
4.
0
3.
5
3.
0
2.
5
2.
0
1.
5
1.
0
0.
5
0.
0
0%
River mile
Figure 4-14. Boulder and cobble substrate composition, summed over 0.1 mile increments upstream from
the mouth of Upper Penitencia Creek (includes both Upper Penitencia Creek and Arroyo Aguague data).
1
Fraction of maximum potential smolt production
0.9
0.8
0.7
0.6
0.5
Current
hypothesized
condition
0.4
0.3
0.2
0.1
0
0
0.01
0.02
0.03
0.04
0.05
0.06
0.07
0.08
0.09
2
Winter habitat quality (fish/ft )
Figure 4-15. Expected smolt production as a function of overwintering habitat quality (i.e., fish density).
0.1
Figure 4-16. Grade control weir at Youth Science Institute in Alum Rock Park. Flow at Dorel gage at time
of photo = 0.51 cfs.
Cfc
Grade control weir at YSI
Modified from Powers and Orsborn (1985).
Figure 4-17. Steelhead leaping ability curves, with YSI grade control weir dimensions superimposed.
100%
% spawning gravel area
90%
% pool area (max depth > 2 ft)
Grade control
weir at YSI
% cobble and boulder area
80%
70%
60%
50%
40%
UUP
URB
ARP
AAG
30%
20%
10%
7
6.
5
6
5.
5
5
4.
5
4
3.
5
0%
River Mile
Figure 4-18. Cumulative percentage of spawning gravel area, pool area, and cobble/boulder substrate
area in Upper Penitencia Creek upstream of RM 3.5 (includes both Upper Penitencia Creek and Arroyo
Aguague data).
100
80
A
95
90
75
85
80
75
70
65
65
60
55
50
60
45
40
55
Daily Mean Flow (cfs)
Daily Average Temperature (˚F)
70
35
50
daily mean flow (cfs)
30
RM 0.1 near Coyote Ck confluence
25
RM 1.2 Education Park Dr.
20
RM 3.3 Percolation Ponds
15
RM 3.7 Noble Ave.
45
10
5
0
Ju
l-0
0
Ju
l-0
0
Ju
l-0
0
Au
g00
Au
g00
Au
g00
Se
p00
Se
p00
Se
p00
O
ct
-0
0
O
ct
-0
0
O
ct
-0
0
N
ov
-0
0
N
ov
-0
0
N
ov
-0
0
D
ec
-0
0
D
ec
-0
0
D
ec
-0
0
M
ay
-0
0
M
ay
-0
0
M
ay
-0
0
M
ay
-0
0
Ju
n00
Ju
n00
Ju
n00
40
Date
100
80
B
95
90
75
85
80
75
70
65
65
60
55
50
60
45
40
55
35
50
30
25
RM 1.3 Mabury Rd.
20
45
15
RM 3.7 Noble Ave.
10
5
Ju
l-0
1
Ju
l-0
1
Ju
l-0
1
Au
g01
Au
g01
Au
g01
Se
p01
Se
p01
Se
p01
O
ct
-0
1
O
ct
-0
1
O
ct
-0
1
N
ov
-0
1
N
ov
-0
1
N
ov
-0
1
D
ec
-0
1
D
ec
-0
1
D
ec
-0
1
0
M
ay
-0
1
M
ay
-0
1
M
ay
-0
1
M
ay
-0
1
Ju
n01
Ju
n01
Ju
n01
40
Date
Figure 4-19. Daily average stream temperatures at monitoring locations in
Upper Penitencia Creek in 2000 (A) and 2001 (B), with available streamflow
data.
70
80
75
100
C
95
90
85
80
70
75
65
65
60
55
60
50
45
40
55
35
50
30
25
RM 1.3 Mabury Rd.
20
15
RM 3.7 Noble Ave.
45
70
10
5
0
M
ay
-0
2
M
ay
-0
2
M
ay
-0
2
M
ay
-0
2
Ju
n02
Ju
n02
Ju
n02
Ju
l- 0
2
Ju
l- 0
2
Ju
l- 0
2
Au
g02
Au
g02
Au
g02
Se
p02
Se
p02
Se
p02
O
ct
-0
2
O
ct
-0
2
O
ct
-0
2
N
ov
-0
2
N
ov
-0
2
N
ov
-0
2
D
ec
-0
2
D
ec
-0
2
D
ec
-0
2
40
Date
80
100
D
95
90
75
85
80
70
75
65
65
60
55
60
50
45
40
55
35
50
30
25
RM 1.3 Mabury Rd.
20
45
70
15
RM 3.7 Noble Ave.
10
5
0
M
ay
-0
4
M
ay
-0
M 4
ay
-0
4
M
ay
-0
4
Ju
n04
Ju
n04
Ju
n04
Ju
l-0
4
Ju
l-0
4
Ju
l-0
4
Au
g04
Au
g04
Au
g04
Se
p04
Se
p04
Se
p04
O
ct
-0
4
O
ct
-0
4
O
ct
-0
4
N
ov
-0
4
N
ov
-0
4
N
ov
-0
4
D
ec
-0
4
D
ec
-0
4
D
ec
-0
4
40
Date
Figure 4-20. Daily average stream temperatures at monitoring locations in
Upper Penitencia Creek in 2002 (C) and 2004 (D), with available streamflow
data.
MAPS
Stillwater Sciences
Appendix A
APPENDIX A: FOCUSED STUDIES
Stillwater Sciences
Appendix A
Table of Contents
APPENDIX A1:
A1.1
A1.2
STEELHEAD POPULATION ESTIMATION ..............................................1
METHODS ........................................................................................................................1
RESULTS .........................................................................................................................3
APPENDIX A2:
STEELHEAD POPULATION DYNAMICS MODELING ............................6
A2.1 METHODS ........................................................................................................................6
A2.1.1
Population Modeling ...............................................................................................6
A2.1.2
Collecting Habitat-specific Information...................................................................7
A2.1.3
Assigning Steelhead Life History Parameters...........................................................7
APPENDIX A3:
A3.1
A3.2
METHODS ......................................................................................................................10
RESULTS .......................................................................................................................11
APPENDIX A4:
A4.1
A4.2
POOL FILLING ..........................................................................................13
METHODS ......................................................................................................................13
RESULTS .......................................................................................................................14
APPENDIX A5:
A5.1
A5.2
SPAWNING GRAVEL PERMEABILITY ..................................................10
OVERWINTERING HABITAT ..................................................................15
METHODS ......................................................................................................................15
RESULTS .......................................................................................................................16
APPENDIX A6:
FISH PASSAGE BARRIERS ......................................................................19
APPENDIX A7: AVAILABLE WATER TEMPERATURE DATA FOR UPPER
PENITENCIA CREEK ...............................................................................................................20
LITERATURE CITED ...............................................................................................................25
List of Tables
Table A1-1. Population estimates of juvenile steelhead by age class and reach with 95 % confidence
limits. .....................................................................................................................................3
Table A2-1. Structure and parameters for modeling of Upper Penitencia Creek steelhead population
dynamics. ...............................................................................................................................8
Table A2-2. Derivations of carrying capacities used in the model. ...................................................9
Table A3-1. Summary of permeability sampling in the Upper Penitencia Creek watershed. ...........11
Table A4-1. Estimates of pool filling in Upper Penitencia Creek. ..................................................14
Table A5-1. Amount of cobble and boulder substrate and percent embeddedness in Upper
Penitencia Creek and Arroyo Aguague, May 2005. ................................................................16
Table A6-1. Potential fish passage barriers in Upper Penitencia Creek as defined by FAHCE (2000),
Abel (2001), and Stillwater Sciences (2005) ¹........................................................................19
List of Figures
Figure A1-1. Density (fish/ ft2) of age 1 and older steelhead and maximum depth (ft) of habitat
units sampled during spring 2005.
Figure A1-2. Density (fish/ ft2) of age 1 and older steelhead and maximum depth (ft) of habitat
units sampled during fall 2005.
Stillwater Sciences
Appendix A
Figure A7-1. Daily average, maximum, and minimum water temperatures recorded at SCVWD
monitoring locations in Upper Penitencia Creek in 2000, with daily mean flow at
the Dorel gage.
the Dorel gage.
the Dorel gage.
the Dorel gage.
Stillwater Sciences
Appendix A
APPENDIX A1: STEELHEAD POPULATION ESTIMATION
A1.1 Methods
Direct observation dives were conducted to estimate the total juvenile steelhead population
in Upper Penitencia Creek and Arroyo Aguague in spring and fall 2005. To develop the
population estimate we used the most recent iteration of two-phase ratio estimation design
developed by Dr. David Hankin, Humboldt State University (Hankin and Mohr, in
preparation). This method estimates total fish abundance in small streams using the
following components: (1) habitat typing of the entire stream channel, (2) stratified random
selection of habitat units to receive at least a single-pass diver count, (3) estimation of fish
abundance in a stratified random selection of these units using the method of bounded
counts, based on four independent diver counts. This last step calibrates the first phase
(step 2) counts of fish by divers using a more intensive, second phase of repeated diver
counts.
An existing habitat database (FAHCE 2000) was used to select habitat units for sampling
and to extrapolate the observed fish densities to the entire stream network. Based on
previous fisheries inventories, which found no juvenile steelhead at sample sites below
River Mile (RM) 3.5 (Li 2000), sampling was restricted to areas above this point. In
addition to Upper Penitencia Creek, the survey included a portion of Arroyo Aguague, the
main tributary to Upper Penitencia Creek. Arroyo Aguague was sampled from its mouth
upstream approximately 0.7 mile to a barrier waterfall. Reconnaissance level field visits
and evidence from a previous fisheries inventory (Li 2000) suggest that Upper Penitencia
Creek may be broken into two reaches: (1) an upper reach of relatively consistent habitat
characterized by a deeply confined valley, moderate channel gradient, and consistent flows
that includes all of Arroyo Aguague and Upper Penitencia Creek below the waterfall
barriers and extends downstream to approximately river mile 6.0; (2) a lower reach with
less confinement, moderate-to-low channel gradient, and decreasing flow volume that
extends from RM 6.0 to RM 3.5 (the lowermost extent selected for sampling). This lower
reach is characterized by sharp gradients in environmental variables, such as stream
temperature and flow volume, that eventually result in poor habitat suitability for steelhead
in the lower portion of the stream. Because of these differences in habitat characteristics,
these stream segments were treated as independent reaches.
Sample site selection followed the “quasi-systematic” methodology described by Hankin
and Mohr. In practice, this method requires the field crew to determine whether the kth
unit is to be included in the first or second phase samples by observing whether or not the
kth number on a continuous list of numbers is either a “1” (included), or a “0” (not
included). These continuous sequences of “1”s and “0”s are generated independently for
each habitat type. Selected habitat units were be located in the field and marked with
aluminum tags. The dimensions of units selected for sampling were measured prior to
snorkeling.
Prior to sampling conducted for population estimation, day and night dive counts were
conducted at selected sample sites to assess differences in observed steelhead density
between day and night surveys. During these preliminary surveys, night counts provided
consistently higher counts of fish ≥ age 1+. Nighttime surveys were therefore selected as
Stillwater Sciences
A-1
Appendix A
the method to be used for population estimates. A critical assumption of the bounded
counts approach is that all individuals have a chance of being observed. Hankin and Mohr
(in press) found that their survey designs were suitable for coho salmon, but they were not
confident about applying their methodology to steelhead juveniles because the fish’s
secretive nature may violate the assumption that all fish have an observation probability >
0. Sampling during the night will help increase observation probabilities, since juvenile
steelhead are less oriented towards cover and less apt to flee from divers at night. Another
result from the day/night snorkeling comparison is that, in contrast to age 1+ fish, detection
of age 0+ fish declined dramatically during the night. Our observations indicated that these
small fish may have moved into shallow habitats along the margins of pools and runs, or
into very shallow riffles—areas that, in general, were too shallow to snorkel. Therefore,
we believe that spring snorkeling may have underestimated the abundance of age 0+
steelhead.
Snorkel surveys were conducted during late-May and mid-October at sample sites located
throughout the rearing reaches of Upper Penitencia Creek. Snorkeling protocols followed
the Method of Bounded Counts (MBC) described in Hankin and Mohr (in press). The
snorkel survey and extrapolated population estimate was stratified by habitat type (i.e.,
pools and runs) because these habitat units have different physical characteristics that
affect the true number of steelhead that may occupy them, as well as our probability of
observing them. Only pool and run habitats were snorkeled. Hankin and Reeves (1988)
showed that snorkel counts are poorly correlated with accurate estimates of fish numbers in
riffles. Our observations also suggest that riffles are too shallow in Upper Penitencia Creek
to snorkel effectively. Dive counts were conducted in approximately 60 pool and run
habitats. With few exceptions, the same habitat units sampled during the spring survey
were sampled during the fall survey. During the fall, we shifted our sampling effort to
include slightly more sample sites in the upper reach of Upper Penitencia Creek and in
Arroyo Aguague, and fewer in the lower reach of Upper Penitencia Creek, since there was
a high frequency of zero counts in the lower reach during the spring.
During snorkel surveys, one diver conducted fish counts in each selected habitat unit. The
diver cautiously entered the lower end of each habitat unit and proceeded upstream to the
top of the unit. The number of fish were counted and identified to species, and were
classified into young-of-the-year (<100 mm), or age 1+ and older fish (>100 mm). This
size break corresponds to age classes observed by Smith (1997) and Li (2000) during
previous surveys in Upper Penitencia Creek. Data were recorded on underwater dive slates
during the dive counts and later transferred to data sheets.
Single-pass dive counts were calibrated to estimate the “true” abundance of fish using the
MBC in a subsample of habitat units. At sites chosen for repeat sampling, a total of four
dive counts were made. Dives were repeated after resting the unit for 10–20 min to allow
water clarity (i.e., visibility) to return to normal.
We used t-tests to determine the statistical significance of differences between spring and
fall population estimates described here. We used multiple regression to determine
relationships between fish density and habitat variables. We also compared our population
estimates to existing population data available from Li (2001). Li sampled during the
period of low flow and warm temperatures in late summer, after the period where any
potential density-dependent mortality or emigration of fish that had survived their first
winter would have occurred. During this effort, eight sites spaced at 0.5 mile (0.8
Stillwater Sciences
A-2
Appendix A
kilometer) intervals between stream mile 2.88 and 5.88 were sampled. Fish densities were
estimated using multiple-depletion electrofishing in one riffle and one pool at each of the
sample sites, for a total of eight pools and eight riffles sampled. Separate fish estimates
were calculated for age 0+ and age 1+ and older steelhead for each habitat type at each site.
We used the densities reported by Li (2001) to extrapolate a population estimate for the
perennial reaches of Upper Penitencia Creek watershed between stream mile 3.5 and barrier
falls in Upper Penitencia Creek and Arroyo Aguague.
A1.2 Results
Fish densities for both age 0+ and age 1+ and older steelhead increased at upstream sample
sites (Figure 4-1 and 4-2) similar to the findings of Li (2000). Fish densities from our
survey also generally agree with those observed by Li in areas where the two surveys
overlapped. Table A1-1 shows the spring and fall population estimates by age class,
habitat type, and reach, with 95 % confidence limits. Results of a statistical comparison of
spring and fall population estimates are also provided.
Table A1-1. Population estimates of juvenile steelhead by age class and reach with 95 %
confidence limits.
Life
stage
Age
0+
Age
1+
and
older
Habitat
Spring 2005
type/total
Estimate
Upper
pools
257
Pen
runs
453
lower
total
711
Upper
pools
478
Pen
runs
1,492
upper
total
1,970
Arroyo
pools
137
Aguague
runs
829
total
966
Upper
pools
165
Pen
runs
178
lower
total
343
Upper
pools
166
Pen
runs
292
upper
total
458
Arroyo
pools
130
Aguague
runs
163
total
293
*
CI = +/-2*SQRT(variance)
Reach
Spring 2005
+/- 95% CI*
198
418
463
169
1,170
1,182
66
507
511
132
150
200
65
158
171
41
79
89
Fall 2005
Estimate
45
196
241
664
1,064
1,728
224
296
520
190
215
405
204
145
348
244
124
368
Fall 2005
+/- 95% CI*
138
109
176
209
356
413
51
110
121
152
205
255
111
207
235
71
51
88
Probability
Spring = Fall
0.088
0.171
0.037
0.153
0.393
0.640
0.016
0.017
0.049
0.804
0.768
0.700
0.522
0.268
0.453
0.011
0.459
0.273
The abundance of age 0+ steelhead declined consistently across stream reaches from spring
to fall (Table A1-1; also see Figure 4-3). In the lower reach of Upper Penitencia Creek,
declines in the densities of age 0+ fish in both pools and runs resulted in a significantly
lower fall estimate (α = 0.05). In the upper reach of Upper Penitencia Creek, slight
increases in density of age 0+ steelhead in pools were offset by larger declines in density in
runs resulting in no significant difference between the spring and fall estimate. In Arroyo
Aguague, fall densities of age 0+ fish were higher than spring densities in pools, but were
Stillwater Sciences
A-3
Appendix A
significantly lower in runs, resulting in a significant net decrease in the reach-specific
population estimate. Overall, the total estimate for age 0+ steelhead in Upper Penitencia
Creek and Arroyo Aguague declined from 3,647 fish in the spring to 2,489 fish in the fall.
The change in the estimated number of age 1+ and older steelhead was variable across
reaches (Table A1-1; also see Figure 4-4). In the lower reach of Upper Penitencia Creek,
fall densities of age 1+ and older steelhead increased slightly in both pool and run habitats,
but these changes did not result in significant changes to the estimated population size. In
the upper reach of Upper Penitencia Creek, increases in the density of age 1 and older
steelhead in pools were offset by decreases in runs, resulting in no significant change in the
population size. In Arroyo Aguague, significant increases in pool densities were offset by
decreases in run densities, resulting in a net increase in the fall estimate, although this
change was not statistically significant. Overall, the total estimate for age 1+ and older
steelhead in Upper Penitencia Creek and Arroyo Aguague was 1,094 in the spring and
1,121 in the fall.
On a unit-by-unit basis, the overall trend was for habitat unit-specific densities of age 1+
and older steelhead to decline in run habitats from spring to fall, whereas the change in
densities of age 1+ and older fish in pools was more variable (Figure 4-2). Spring and fall
densities of age 1 and older steelhead were positively related to habitat depth (Figure A1-1
and A1-2). In a linear regression depth explained 34 percent of the variation in spring
density of age 1 and older steelhead (F = 30.19, p < 0.01), and 29 percent of the variation
in fall density of age 1 and older steelhead (F = 22.80, p < 0.01).
Estimates derived from our spring and fall snorkel surveys are based on fish densities
observed in run and pool habitats only. However, using electrofishing Li (2001) found age
0+ and age 1+ steelhead in riffles. To compare with Li’s population estimates of age 1+
fish, we applied the densities of fish we observed in runs to the extent of riffle habitat
present above stream mile 3.5. This resulted in a slightly higher spring estimate of 1,300
age 1+ steelhead compared to our initial estimate of approximately 1,060 age 1+ steelhead.
The fall estimate increased from 1,121 to 1,475 fish. Conversely, since Li (2001) sampled
only riffle and pool habitat, we applied the reach specific densities of age 0+ and age 1+
steelhead that he observed in riffles to the extent of run habitat in each reach. When
combined with extrapolated estimates based on habitat specific densities for riffle and pool
habitats this resulted in a total population estimate of 1,100 age 1+ and older steelhead.
In both our spring and fall surveys and Li’s survey, all age 1 and older fish were considered
together for the purpose of estimating the juvenile steelhead population. Our field
observations indicate that age 2+ and older fish constituted a relatively small percentage of
the 2005 population estimates, comprising approximately 5 percent (spring estimate) to 10
percent (fall estimate) of the age 1 and older fish observed.
Stillwater Sciences
A-4
Appendix A
0.04
0.035
pools
runs
Spring density (fish/ft^2)
0.03
0.025
0.02
0.015
0.01
0.005
0
0
1
2
3
4
5
6
Maximum depth (ft)
Figure A1-1. Density (fish/ ft 2 ) of age 1 and older steelhead and maximum depth (ft) of
habitat units sampled during spring 2005.
0.06
0.05
pools
runs
Fall density (fish/ft^2)
0.04
0.03
0.02
0.01
0
0
1
2
3
4
5
6
Maximum depth (ft)
Figure A1-2. Density (fish/ ft 2 ) of age 1 and older steelhead and maximum depth (ft) of
habitat units sampled during fall 2005.
Stillwater Sciences
A-5
Appendix A
APPENDIX A2: STEELHEAD POPULATION DYNAMICS
MODELING
A2.1 Methods
A preliminary assessment of current habitat conditions for steelhead populations in the
Upper Penitencia Creek watershed was conducted within the framework of a population
dynamics model. This assessment relies on fundamental concepts in population dynamics,
particularly stock-production analysis. The assessment performed here was based on a
combination of results from field studies conducted by Stillwater Sciences and existing
habitat data from Upper Penitencia Creek (i.e., FAHCE 2000) and is only intended to
provide a preliminary, and conservative, indication of the degree to which steelhead smolt
production may be limited by current channel conditions.
The population modeling exercise involved three basic steps: (1) analyzing habitat-specific
information regarding habitat quality and quantity from a suitable reach within the area of
interest; (2) assigning density-independent survival and habitat-specific carrying capacity
values for each salmonid life stage; and (3) integrating these values into a system of
equations to express the impact of current salmonid habitat conditions on potential
steelhead production. These three steps are described in further detail below (in reverse
order).
A2.1.1
Population Modeling
The salmonid population modeling approach used in this analysis is based on stockproduction theory (Ricker 1976). Stock-production theory characterizes the number of
individuals of one life stage at one time (the production) as a function of the number in the
same cohort of an earlier life stage at an earlier time (the stock). This approach is
particularly well suited to situations where physical habitat is believed to be limiting, and
where population dynamics can be plausibly separated into density-independent and
density-dependent components, such as productivity (the ratio of stock to production that
would be expected if there were no limits on population density) and carrying capacity (the
maximum number of individuals of a given life stage that the habitat can support for the
duration of that life stage).
The population model uses the following relationships between a stock S and a production
P . In the equations below, the parameter r can generally be interpreted as the intrinsic
productivity (e.g., a density-independent survival rate, or in the case of reproduction, a
fecundity). The parameter K is interpreted as the carrying capacity for the production
stage. In practice, both of these can vary from year to year in response to varying
environmental conditions, although such refinements were not used in the present analysis.
All of these relationships are asymptotic to the two lines P = rS and P = K . There are three
basic types of functional relationships that are used in this model:
Truncated Linear:
Modified Beverton-Holt:
P = max(rS , K )
P=
((rS )
rKS
γ
+Kγ
)γ
1
Stillwater Sciences
A-6
Superimposition:
Appendix A
P = K (1 − exp( − rS K ) )
The truncated linear relationship is often used when no natural carrying capacity is evident;
in this case K is set to some very large value, or simply omitted. The parameter γ of the
modified Beverton-Holt relationship controls the “stiffness” of the relationship: γ = 1 is the
usual Beverton-Holt relationship; larger values yield curves which make more abrupt
transitions between the two asymptotes P = rS and P = K . The superimposition relationship
was derived from analytical models of habitat selection.
A2.1.2
Collecting Habitat-specific Information
Habitat-specific information for this population modeling exercise was collected during
1998 by SCVWD and Entrix (FAHCE 2000) and included the entire stream channel of
Upper Penitencia Creek. Basic habitat types (i.e., pool, riffle, run, and cascade) were
delineated within the surveyed area according to standard habitat mapping descriptions.
Mean length, width, and depth were estimated for each habitat unit, and maximum depth
was measured within each unit. The percentage of habitat area composed of the dominant
and subdominant substrate categories (i.e., silt, sand, gravel, cobble, boulder) were
estimated for each habitat unit. In addition to these habitat parameters, the area of potential
steelhead spawning habitat (if present) was estimated. Spawning habitat area estimates
were based on professional judgments of steelhead spawning habitat requirements (J. Abel,
SCVWD, pers. comm.). We collected additional field data on substrate embeddedness
during focused studies to characterize winter habitat conditions in Upper Penitencia Creek
and Arroyo Aguague (Appendix A5). We also collected habitat data for the previously
unmapped reach of Arroyo Aguague from its mouth to the barrier waterfall located
upstream approximately 0.7 mi using protocols derived from the FAHCE database.
A2.1.3
Assigning Steelhead Life History Parameters
Steelhead life history was separated into discrete stages having identifiable, and to some
extent overlapping, habitat requirements. As discussed above, the population dynamics
modeling approach that we used requires two biological parameters for each stage: (1) a
carrying capacity (K), which describes the ultimate limits imposed by crowding and
competition; and (2) an intrinsic productivity (r), which describes the expected dynamics
under conditions for which the effects of crowding and competition can be ignored. The
model was parameterized using values obtained from focused field studies (e.g.,
permeability measurements) that related physical habitat measurements to survival (r) or
density-related carrying capacities (K). Existing information for Upper Penitencia Creek
was not available for some life stages so professional judgment was used to determine
when literature based values fish densities were reasonable surrogates for data specific to
Upper Penitencia Creek. In all cases, literature-based values were compared to fish
densities observed during studies by Li (2000), SCVWD (FAHCE 2000), and snorkel
surveys conducted during this survey (Appendix A1). Tables A2-1 and A2-2 summarize the
K and r parameters used in the analysis, and the derivations of these values.
Stillwater Sciences
A-7
Appendix A
Table A2-1. Structure and parameters for modeling of Upper Penitencia Creek steelhead
population dynamics.
Life history segment
Stock-production
relationship
r (fish/fish)
a
K (fish)
7,072,455 b
Spawning and superimposition
(spawner to effective eggs)
Superimposition
2,751.5
Egg and alevin rearing
(effective egg to spring fry)
Truncated Linear
0.39c
(NA)
Early fry rearing
(spring fry to 0+ summer)
Modified BevertonHolt ( γ = 2 )
1
31,269d
Summer rearing, first year
(0+ summer to 0+ fall)
Truncated Linear
1
2,712e
Winter rearing, first year
(0+ fall to 1+ spring)
1
1,500f
Summer rearing, second year
(1+ spring to 1+ fall)
1
1,437 g
Winter rearing, second year
(1+ fall to 2+ smolt)
1
500 h
Outmigration, ocean life, and return
(2+ smolt to spawner)
Truncated Linear
0.05i
(NA)
a.
b.
c.
d.
e.
f.
g.
h.
i.
0.5 females/total spawners × 5,503 eggs/female (estimated from Shapovalov and Taft 1954)
6,426 ft² spawning habitat × 0.2 redds/ft² × 5,503 eggs/redd.
Derived from permeability samples (Appendix A3).
See Table A2-2.
Derived from age 0+ and older steelhead densities from fall 2005 population estimate.
Derived from spring estimates of age 1+ and older steelhead in 2005 and field measurements of winter habitat quality.
Derived from age 1+ and older steelhead densities from Li (2001) and fall 2005 population estimate.
Derived from age 0+ winter carrying capacity scaled for larger age 1+ steelhead in 2005, and from estimates of smolt
production in 1999 and 2000 (FAHCE 2000).
Shapovalov and Taft (1954).
Stillwater Sciences
A-8
Appendix A
Table A2-2. Derivations of carrying capacities used in the model.
Life history segment
Early fry rearing
Habitat type
Habitat area
(ft²) a
b
Density
(fish/ft²)
Pool
52,384
Riffle
70,830 c
0.1433 h
Run
107,001 d
0.1437 i
Pool
52,384b
0.0132 k
Riffle
70,830 c
0.0146 l
Run
107,001 d
0.0091 l
Winter rearing, first year
All
44,349 e
0.0338 j
Summer rearing, second year
Pool
50,085f
0.0100 k
Riffle
70,830 c
0.0050 l
1,424
Run
All
107,001 d
48,061 e
0.0053 l
0.0104 m
500
Summer rearing, first year
Winter rearing, second year
a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
k.
l.
m.
0.1095
K (fish)
g
31,269
2,712
1,500
All area estimates based on FAHCE (2000) for Upper Penitencia Creek and on data collected by Stillwater Sciences
in 2005 for Arroyo Aguague.
Total pools upstream of RM 3.5
Total riffles upstream of RM 3.5
Total runs upstream of RM 3.5
Area of cobble/boulder substrate above mile 3.5 allocated to specific steelhead age classes based on winter habitat
survey results (Appendix A5).
Pools with summer maximum depth of at least 1 ft
1.179 fish/m² (Connor 1996) × 0.3048 m²/ft²
1.543 fish/m² (Connor 1996) × 0.3048 m²/ft²
1.547 fish/m² (Connor 1996) × 0.3048 m²/ft²
Derived from observed spring age 1+ population estimate (Appendix A1) and winter habitat survey results (Appendix
A5).
Weighted average of observed age-specific density in pools in reaches sampled during 2005 population estimates.
Weighted average of observed age-specific density in runs in reaches during 2005 population estimates.
Ratio of age 0+ to age 1+ fish length was used as a scaling factor to approximate the degree to which fewer larger fish
can fit in a given habitat area. Fish size was estimated from data reported in FAHCE (2000), and Li (2001).
Stillwater Sciences
A-9
Appendix A
APPENDIX A3: SPAWNING GRAVEL PERMEABILITY
A3.1 Methods
To determine the quality of streambed gravels for salmonid egg incubation and larval
(alevin) rearing, substrate permeability (i.e., hydraulic conductivity) was measured using a
modified Mark IV standpipe (Terhune 1958, Barnard and McBain 1994). Gravels at
potential spawning sites were mixed to a depth of 0.95 feet to simulate mixing and sorting
conditions that would occur during redd construction by a spawning salmonid (see Kondolf
and Wolman 1993 for more information on this topic). The standpipe used was 46.5 inches
long, with a 1.0 in inside diameter and a 1.25 in outside diameter. The standpipe had a 2.75
in-long band of perforations and was driven into the substrate so that the band of
perforations extended in depth from approximately 0.60 to 0.86 ft below the bed surface.
To reduce the potential for water ‘slippage’ down the pipe, the standpipe was held, but not
forced in any direction, during the driving process.
Permeability was measured by using a Thomas vacuum pump (Model 107CDC20, powered
by a 12-volt rechargeable battery) to siphon water out of the standpipe to maintain the
water level inside the standpipe exactly one-inch lower than the surrounding water. By
measuring the volume of water siphoned out of the standpipe over a measured time
interval, it was possible to determine the recharge rate of the water level in the standpipe
under a standard one-inch pressure head. At each spawning patch assessed, the standpipe
was driven in once and five consecutive permeability measurements were taken. We used
the median permeability value from this series of measurements for further analysis.
The recharge rate (units of volume per time) data measured in the field were converted into
permeability (units of length per time) using an empirically derived rating table (Barnard
and McBain 1994) and adjusted with a correction factor that accounts for temperature
related changes in water viscosity that can affect permeability results (Barnard and McBain
1994).
We then used published empirical relationships between permeability and survival-toemergence for anadromous salmonids (McCuddin 1977, Taggart 1976) to estimate survival
based on our permeability measurements. The following simple linear regression defines
this relationship:
Survival = 0.1488 * ln(Permeability) - 0.8253
where permeability is in units of cm/hr.
During field studies we observed several redds constructed in the tails of pools. When we
encountered a redd we measured the maximum width and total length of the pit and tail.
The area of each redd was then approximated by calculating the area of an ellipse using the
width as the short axis and the total redd length as the long axis.
Stillwater Sciences
A-10
Appendix A
A3.2 Results
The results of the permeability analysis and the survival index calculation are given in Table A31. Discussion of the results is provided in Section 5.3.1 of the main report.
Table A3-1. Summary of permeability sampling in the Upper Penitencia Creek watershed.
Reach
UUP2
ARP1
ARP2
ARP3
URB1
URB2
AAG
Site ID
3
2
1
1
2
3
4
5
6
13
12
11
10
9
8
7
6
5
4
3
2
1
9
8
7
6
5
4
3
2
1
10
9
8
7
6
5
River Mile
6.7
6.7
6.7
6.6
6.5
6.5
6.4
6.3
6.3
6.1
6.1
5.9
5.4
5.3
5.0
4.9
4.7
4.6
4.4
4.3
4.1
4.1
3.5
3.4
3.2
3.0
3.0
2.6
2.5
2.4
2.3
-------
Date
5/20/2005
5/20/2005
5/20/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/23/2005
5/19/2005
5/19/2005
5/19/2005
5/19/2005
5/19/2005
5/19/2005
5/19/2005
5/19/2005
5/19/2005
5/19/2005
5/19/2005
5/20/2005
5/20/2005
5/20/2005
5/20/2005
5/20/2005
5/20/2005
Permeability
(cm/hr)
1,540
2,512
2,426
1,490
2,154
4,436
4,817
13,593
7,248
4,612
4,933
3,953
21,203
37,507
1,629
2,234
12,600
8,005
2,462
1,979
933
2,072
1,362
2,435
8,814
8,278
4,523
4,523
6,847
3,632
2,526
4,727
2,208
1,413
3,082
2,699
1,258
Predicted survivalto-emergence
0.27
0.34
0.33
0.26
0.32
0.42
0.44
0.59
0.50
0.43
0.44
0.41
0.66
0.74
0.28
0.32
0.58
0.51
0.34
0.30
0.19
0.31
0.25
0.33
0.53
0.52
0.43
0.43
0.49
0.39
0.34
0.43
0.32
0.25
0.37
0.35
0.24
Stillwater Sciences
A-11
Reach
Site ID
4
3
2
1
Appendix A
River Mile
-----
Date
5/20/2005
5/20/2005
5/20/2005
5/20/2005
Permeability
(cm/hr)
2352
1,829
2,865
4,237
Predicted survivalto-emergence
0.33
0.29
0.36
0.42
Stillwater Sciences
A-12
Appendix A
APPENDIX A4: POOL FILLING
A4.1 Methods
To determine the impact of pool filling by fine sediment in the study reaches, we developed
a rapid technique for estimating pool filling based on the V* technique developed by Hilton
and Lisle (1993). The rapid technique is similar to the V* technique in that it estimates the
proportion of the residual pool filled by fine sediment, where “residual pool” is defined as
the scoured volume of the pool lying below the downstream grade control. A validation
experiment showed that results using the rapid method of assessing pool filling was
consistently within 10 percent of results using the more rigorous Lisle and Hilton’s V*
method. Details of the validation can be found in Stillwater Sciences and Dietrich (2002).
The rapid method involves estimating the volume of the residual pool by measuring the
length, average width and maximum depth of water to determine the volume of water in the
pool. The bottom of the pool was then probed extensively to identify the locations and
surface areas of all patches of fine sediment within the residual pool. The depth of each
patch of fine sediment was then measured in five locations to calculate the average depth of
the deposit. Finally, a detailed sketch of each pool was drawn, showing the outline of the
residual pool, location of fine sediment deposits, location of pool depth measurements, and
any significant landmarks (e.g., riprap or large trees) that would be useful for locating the
pool in the future.
Using the modified method, pool filling by fine sediment was calculated by dividing the
estimated volume of fine sediments in each pool by the sum of the water volume and fine
sediment volume.
n
∑Ad
Pool filling (PF) =
i
i =1
i
n
∑Ad
i =1
i
i
+V
where Ai is the surface area, di is the depth of the ith sediment patch in the pool, and V is
the total pool water volume.
As suggested by Hilton and Lisle (1993), a volume weighted mean was the statistic used to
characterize pool filling by fine sediment at the reach level.
n
Volume Weighted, Reach Averaged Pool Filling
=
∑ PF
i
⋅ PVi
i =1
∑ All Pool Volumes
Where PFi is the pool filling and PVi is the volume of the ith pool. In the analysis, pool
shapes were assumed to be elliptical cylinders and sediment deposits were assumed to be
planar ellipses.
Stillwater Sciences
A-13
Appendix A
In considering pool filling, we focused our studies in the area from Arroyo Aguague and
Upper Penitencia Creek upstream of its confluence with Arroyo Aguague to URB1 (RM
3.5–6.7). This length was selected for focused studies because it is known to provide
habitat to steelhead, and is the extent of the perennially wetted creek in most years. After
obtaining permission to access the channel, a total of 21 pools were surveyed. Photographs
were taken and GPS positions were recorded at each pool using a handheld Garmin GPS
device. Then, each pool was assessed to estimate filling by fine sediment. Permeability
was sampled in the same reaches of the creek.
A4.2 Results
The results of the pool filling analysis are shown in Table A4-1. Pools were numbered in
the sequence in which they were assessed. Discussion of the results is provided in Section
4.2.2 of the main report.
Table A4-1. Estimates of pool filling in Upper Penitencia Creek.
Site
Description
UTM (NAD 27)
Easting
RM
Date
Max
Depth
(ft)
Pool
Volume
(ft 3)
Sediment
Volume
(ft 3)
Pool
Filling
(%)
Northing
AAG
AAG
AAG
AAG
UUP2
UUP2
UUP2
ARP1
ARP1
0607491
0607447
0607389
0606940
0606977
N/A
N/A
0606901
0606619
4139608
4139887
4140037
4140269
4140469
N/A
N/A
4140384
4140092
7.00
6.90
6.80
6.70
6.78
6.75
6.71
6.63
6.32
6/9/2005
6/9/2005
6/9/2005
6/9/2005
6/8/2005
6/8/2005
6/8/2005
6/8/2005
6/9/2005
2.9
2.9
2.1
1.6
1.6
1.2
0.8
1.3
1.8
1,450.5
1,292.0
420.6
606.5
179.1
59.4
19.0
156.2
757.6
176.8
33.8
2.5
17.5
19.5
1.8
1.2
6.7
29.4
12.2
2.6
0.6
2.9
10.9
3.1
6.5
4.3
3.9
ARP1
0606484
4139917
6.18
6/9/2005
1.8
281.8
12.3
4.4
ARP2
ARP2
ARP2
ARP3
ARP3
ARP3
URB1
URB1
URB1
URB1
URB1
0606449
0605958
0605324
0604811
0604536
0604064
0603643
0603524
0603542
0603365
0603286
4139634
4139542
4139378
4139189
4139274
4139547
4139305
4139216
4139211
4139195
4139144
6.04
5.65
5.26
4.87
4.68
4.28
3.87
3.79
3.65
3.65
3.59
6/8/2005
6/8/2005
6/8/2005
6/7/2005
6/7/2005
6/7/2005
6/7/2005
6/9/2005
6/7/2005
6/7/2005
6/7/2005
2.0
2.5
2.0
1.3
1.5
2.0
1.4
1.2
1.1
1.2
1.2
377.0
1,372.2
375.7
315.0
317.9
565.5
518.4
502.7
232.6
130.8
173.7
84.2
105.9
20.7
3.4
20.3
13.5
56.5
10.8
12.9
8.7
19.2
22.3
7.7
5.5
1.1
6.4
2.4
10.9
2.2
5.6
6.6
11.1
Stillwater Sciences
A-14
Appendix A
APPENDIX A5: OVERWINTERING HABITAT
A5.1 Methods
Field-based habitat mapping was conducted in Upper Penitencia Creek to assess winter
habitat suitability for juvenile steelhead. Habitats were classified by type (e.g., run, riffle,
or pool), following the protocol used in FAHCE (2000). Mapping within each study reach
was continuous, with each habitat unit abutting the next. To be classified as an independent
unit, the unit had to contain a distinctly different habitat type, with its length equal to or
greater than the active channel width (McCain et al.1990).
In each habitat unit, the dominant and subdominant substrate types were identified based on
the length of the intermediate axis of the dominant particle size. Substrates were classified
as bedrock, boulder (>10 in), cobble (2.5 to 10 in), gravel (0.25 to 2.5 in), sand (<0.25 in),
or silt (FAHCE 2000).
For those habitat units containing cobble and/or boulder, substrate embeddedness was
estimated by removing several sediment particles (i.e., cobble or boulder) to determine the
percentage of the circumference covered by smaller sediments. A slight discoloration of the
particles is typically apparent above and below the level of embeddedness. If the surficial
particle was greater than 10% embedded, no additional assessments were conducted. If the
surficial particle was less than 10% embedded, the surface layer of substrate was excavated
using a hand trowel to determine the depth of large diameter surface particles and the
degree to which subsurface cobble or boulder were embedded in finer substrates.
Levels of coarse substrate embeddedness were related to their ability to support juvenile
steelhead during the winter using relationships developed from laboratory flume studies
(see Table 4-5) and spring 2005 population estimates derived from direct observation dives
(which provide a minimum estimate of winter survival). The fish densities estimated from
this analysis were then extrapolated to the portion of the stream channel composed of
cobble and boulder substrate as estimated from an existing habitat database (FAHCE 2000).
Because the available winter habitat must be partitioned among at least two age classes of
juvenile steelhead, adjustments to fish densities approximate this partitioning. If all habitat
is allocated to 0+ juveniles, or all to 1+ juveniles, there will be no net production. We have
resolved this by simply assuming that the 0+ and 1+ juveniles partition the habitat in such a
way as to maximize the overall smolt production when winter habitat is saturated.
Additionally, we assume that even in cases where all habitat is usable by both age 0+ and
age 1+ steelhead, a given habitat area will support a higher age 0+ winter carrying capacity
compared to the capacity for age 1+ fish because age 1+ fish are larger. Therefore, we
partitioned the density of juvenile steelhead among age 0+ and 1+ age classes while
considering allometric influences on their densities using observed age specific fish sizes.
This resolution is conservative in the following sense: if analysis using this assumption
indicates that winter habitat is limiting, than this will also be true of any more elaborate
analysis incorporating intra-specific competition and more complex allocation rules.
We used the estimates of rearing densities and habitat area to compare with observed fish
densities from spring 2005 and previous fisheries surveys in Upper Penitencia Creek to
allocate the available winter habitat between multiple steelhead age classes (Appendix A5). Based on this analysis we assigned approximately 48,061 ft2 of the available
Stillwater Sciences
A-15
Appendix A
cobble/boulder habitat to age 1+ steelhead, and 44,349 ft2 to age 0+ steelhead. This
resulted in approximately 20 % of the cobble/boulder area estimated by FAHCE (2000)
being removed from the winter habitat area estimate. Using these habitat areas and rearing
densities estimated from substrate embeddedness levels to estimate carrying capacities
approximated the fish population estimates derived from this and previous surveys.
A5.2 Results
The winter habitat quality assessment was used in combination with estimates of total
cobble/boulder area provided in FAHCE (2000) to estimate the influence of winter habitat
on overall steelhead production using the population model presented in Appendix A2.
Figure 4-14 (in main report) shows the distribution of cobble and boulder substrate in
Upper Penitencia Creek and Arroyo Aguague. Cobble or boulder material comprised a
large percentage of the stream channel in all reaches. Boulder substrate was especially
abundant above RM 5.0.
The results of the winter habitat survey are presented in Table A5-1. Surface embeddedness
of coarse substrate (i.e., cobble and boulder) was 10% or less in only four of the units
surveyed. In these cases, subsurface embeddedness was found to range from 50 to 80%. No
longitudinal trends in embeddedness were observed. The high level of surface
embeddedness suggests that, despite a high percentage of coarse material within the stream
channel, winter habitat quality for steelhead is relatively low in Upper Penitencia Creek
due to a lack of interstitial refuge. Methods for how this information was used in the
context of a population model are described in Appendix A2.
Table A5-1. Amount of cobble and boulder substrate and percent embeddedness in Upper
Penitencia Creek and Arroyo Aguague, May 2005.
RM
Survey
Location
AAG
begin
end
6.7
7.4
Substrate
Habitat
type
Length
Width
Riffle
Run
Riffle
Pool
Riffle
Pool
Run
Riffle
Pool
Riffle
Run
Pool
Riffle
Pool
Riffle
Pool
Riffle
Pool
72
80
143
58
265
18
99
201
39
450
203
30
202
29
255
26
48
26
21
19
18
18
18
18
17
15
11
16
21
25
16
16
15
14
13
9
%
cobble
40
5
50
20
25
20
15
5
40
5
5
60
15
35
5
35
5
%
boulder
20
20
5
60
25
20
80
5
35
5
%
embedded
surface/
subsurface
20
30
10/50
Embedding
substrate
sand/gravel
sand/gravel
sand/silt
35
sand/gravel
30
20
sand/gravel
sand/gravel
10/50
25
sand/gravel
sand/gravel
35
25
gravel/sand
50
10
35
5
15
gravel/sand
15
sand/gravel
Stillwater Sciences
A-16
RM
Survey
Location
UUP2
ARP1
ARP2
begin
8.1
end
6.7
6.7
6.2
6.2
5.1
Appendix A
Substrate
Habitat
type
Length
Width
Riffle
Run
Pool
Riffle
Pool
Riffle
Pool
Run
Pool
Run
Riffle
Pool
Riffle
Run
Pool
Riffle
Pool
Riffle
Pool
125
54
37
62
25
80
25
275
37
617
100
45
75
28
30
159
58
24
35
16
15
12
20
11
19
13
20
14
13
12
10
17
13
9
22
12
17
28
Riffle
13
Run
Pool
Cascade
Pool
Pool
Riffle
Pool
Run
Pool
Pool
Run
Pool
Riffle
Pool
Run
Pool
Run
Riffle
Run
Riffle
Pool
Riffle
Run
Pool
Run
Pocket
Water
%
cobble
45
40
5
35
5
35
%
embedded
surface/
subsurface
15
10/60
Embedding
substrate
30
30
%
boulder
40
25
35
50
20
30
15
35
20
40
55
10
5
65
10
35
gravel/sand
10
55
25
gravel/sand
30
10
60
10
20
gravel
9
0
10
25
34
12
18
34
15
36
12
62
19
26
25
24
25
13
26
22
20
32
60
18
16
96
78
20
28
12
8
9
16
20
7
15
8
9
5
5
8
6
7
7
22
7
6
12
14
10
12
7
14
10
10
5
10
10
5
25
5
25
5
<5
0
<5
5
5
<5
<5
20
45
10
35
10
35
40
5
40
25
25
50
30
10
25
5
30
25
<5
0
<5
5
20
0
<5
10
0
5
20
5
15
5
<5
10
25
40
35
25
40
20
5
25
40
15
N/A
15
30
25
25
20
25
10/80
40
20
35
20
15
30
25
sand/gravel
sand
gravel
gravel/sand
sand/gravel
gravel/sand
sand/gravel
sand/gravel
gravel/sand
sand/gravel
sand/gravel
gravel/sand
gravel/sand
sand/gravel
36
9
15
45
25
sand/gravel
40
sand/gravel
gravel/sand
25
gravel/sand
25
gravel/sand
25
sand/gravel
35
40
gravel/sand
gravel/sand
small
gravel/sand
sand/silt
sand/silt
sand/gravel
sand/silt
sand/silt
sand/silt
gravel/sand
sand/gravel
sand/gravel
sand/gravel
Stillwater Sciences
A-17
RM
Survey
Location
begin
end
ARP3
5.1
3.9
URB1
3.9
3.1
Appendix A
Substrate
Habitat
type
Length
Width
Riffle
Riffle
Run
Riffle
Run
Riffle
Riffle
Pool
Pool
Riffle
Run
Riffle
Run
Riffle
Run
Pool
Riffle
Run
Pool
Riffle
Riffle
Run
Riffle
Run
Riffle
Run
Riffle
Run
Riffle
Run
Riffle
24
53
15
47
76
58
22
14
16
44
10
16
16
23
10
17
11
74
20
25
40
31
31
69
21
20
58
51
15
31
20
7
9
10
10
14
10
13
9
10
11
12
9
8
7
7
7
6
10
12
12
12
10
8
7
6
11
12
8
8
8
5
%
cobble
40
60
25
60
25
35
20
15
20
35
15
30
40
50
40
30
15
15
10
60
40
<5
40
40
40
65
70
60
50
70
90
%
boulder
30
20
5
20
10
35
75
75
5
5
5
10
10
10
5
<5
55
<5
30
10
5
0
5
10
<5
5
10
10
20
<5
5
%
embedded
surface/
subsurface
35
35
40
40
45
20
20
25
30
35
25
30
35
30
60
50
30
40
30
15
30
45
35
30
35
30
25
30
25
35
15
Embedding
substrate
sand/gravel
sand/gravel
sand/gravel
sand/gravel
sand/gravel
sand/gravel
gravel/sand
gravel/sand
sand/silt
sand/silt
sand/gravel
sand/gravel
sand/gravel
sand/gravel
sand/gravel
sand/gravel
sand/silt
sand/gravel
sand/silt
sand/silt
sand/gravel
sand/gravel
gravel/sand
sand/gravel
sand/gravel
sand/gravel
sand/gravel
sand/gravel
gravel/sand
sand/gravel
sand/gravel
Stillwater Sciences
A-18
Appendix A
APPENDIX A6: FISH PASSAGE BARRIERS
Table A6-1. Potential fish passage barriers in Upper Penitencia Creek as defined by FAHCE
(2000), Abel (2001), and Stillwater Sciences (2005).
FAHCE/SWS
Barrier ID
RM
GB1
0.0
GB2
1.3
GB19
1.5
GB15
1
2
3
Location
confluence with Coyote
Creek
Mabury Road diversion
structure
Barrier Description
Barrier
Degree
Priority
critical riffle
Partial
1
diversion structure, with
fish ladder
Intermittent
5
none specified
dryback zone
Intermittent
4
1.7
Penitencia Creek Park
diversion
culvert
Intermittent
2
GB16
2.0
Hwy 680 crossing
critical riffle
Partial
1
GB3
3.6
diversion structure, with
fish ladder
Intermittent
5
GB17
3.9
Noble Ave Diversion
structure
Dorel Drive gaging
station
gaging weir
Unknown
5
GB4
4.9
Quail Hollow1
low flow vehicle crossing
Partial
2
GB18
5.9
YSI drop structure
concrete grade control weir
Partial
1
GB5
6.4
recreational weir
Partial
0
GB20
ND 2
culvert
Partial
3
UP01 3
6.8
waterfall
Complete
ND 2
AA01 3
0.7
waterfall
Complete
ND 2
Alum Rock Falls
(Alum Rock Park)
Berryessa Industrial
Park Bridge Culvert
Upper Penitencia
waterfall
Arroyo Aguague
waterfall
This barrier was removed in 2004
ND = no data or not rated
Barrier ID designated during Stillwater Sciences (2005) field reconnaissance.
Stillwater Sciences
A-19
Appendix A
60
55
RM 1.3 Mabury Rd.
daily max
daily min
ec
D
ov
ec
D
ov
N
ct
ec
D
ov
N
ct
O
Se
p
Au
g
Ju
l
40
Figure A7-1. Daily average,
maximum, and minimum water
temperatures recorded at SCVWD
monitoring locations in Upper
Penitencia Creek in 2000, with
daily mean flow at the Dorel gage.
Flow (cfs)
65
Ju
n
Temperature (˚F)
70
ay
O
ec
75
M
Au
g
40
Date
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
80
45
N
45
Date
85
50
RM 3.7 Noble Ave.
daily max
daily min
50
D
ov
N
ct
O
Se
p
Au
g
l
Ju
Ju
n
M
ay
40
55
l
45
60
Ju
daily max
daily min
65
Ju
n
60
70
Temperature (˚F)
65
75
M
Temperature (˚F)
70
80
ay
75
85
Flow (cfs)
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
80
50
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
Date
85
55
O
ec
Date
ct
40
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
Flow (cfs)
45
D
ov
N
ct
O
Se
p
Au
g
l
Ju
Ju
n
M
ay
40
50
Se
p
45
daily max
daily min
Se
p
50
55
Au
g
daily max
daily min
l
55
60
Ju
60
65
Ju
n
65
70
M
Temperature (˚F)
70
75
Temperature (˚F)
75
80
ay
80
85
Flow (cfs)
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
85
Flow (cfs)
APPENDIX A7: AVAILABLE WATER TEMPERATURE DATA
FOR UPPER PENITENCIA CREEK
Date
Stillwater Sciences
A-20
45
Date
65
60
55
RM 1.3 Mabury Rd.
daily max
daily min
ec
D
ov
N
ec
D
ov
N
O
ct
ec
D
ov
N
ct
O
Se
p
Au
g
Ju
l
40
Ju
n
Temperature (˚F)
70
Flow (cfs)
75
ay
Au
g
40
ec
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
80
M
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
Date
85
45
ct
45
Date
50
RM 3.7 Noble Ave.
daily max
daily min
50
D
ov
N
O
ct
Se
p
Au
g
l
Ju
Ju
n
M
ay
40
55
l
45
60
Ju
daily max
daily min
65
Ju
n
60
70
Temperature (˚F)
65
75
M
Temperature (˚F)
70
80
ay
75
85
Flow (cfs)
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
80
50
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
Date
85
55
O
ec
40
D
ov
N
ct
O
Se
p
Au
g
Ju
l
n
Ju
M
ay
40
50
Se
p
45
daily max
dail min
Se
p
50
55
Au
g
daily max
daily min
l
55
60
Ju
60
65
n
65
70
M
ay
Temperature (?F)
70
75
Ju
75
80
Temperature (˚F)
80
85
Flow (cfs)
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
85
Flow (cfs)
Appendix A
Flow (cfs)
Date
Stillwater Sciences
A-21
45
65
60
55
RM 1.3 Mabury Rd.
daily max
daily min
ec
D
ov
ec
D
ov
N
ct
O
ec
D
ov
N
ct
O
Se
p
Au
g
Ju
l
40
Ju
n
Temperature (˚F)
70
Flow (cfs)
75
ay
Au
g
40
ec
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
80
M
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
Date
85
45
N
45
Date
50
RM 3.7 Noble Ave.
daily max
daily min
50
D
ov
N
ct
O
Se
p
Au
g
l
Ju
Ju
n
M
ay
40
55
l
45
60
Ju
daily max
daily min
65
Ju
n
60
70
Temperature (˚F)
65
75
M
Temperature (˚F)
70
80
ay
75
85
Flow (cfs)
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
80
50
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
Date
85
55
O
ec
Date
ct
40
D
ov
N
ct
O
Se
p
Au
g
l
Ju
Ju
n
M
ay
40
50
Se
p
45
daily max
daily min
Se
p
50
55
Au
g
daily max
daily min
l
55
60
Ju
60
65
Ju
n
65
70
M
Temperature (˚F)
70
75
Temperature (˚F)
75
80
ay
80
85
Flow (cfs)
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
85
Flow (cfs)
Appendix A
Flow (cfs)
Date
Stillwater Sciences
A-22
Appendix A
No data were recorded at SCVWD monitoring
locations in Upper Penitencia Creek in 2003.
Stillwater Sciences
A-23
45
65
60
55
RM 1.3 Mabury Rd.
daily max
daily min
ec
D
ov
ec
D
ov
N
ct
O
ec
D
ov
N
ct
O
Se
p
Au
g
Ju
l
40
Ju
n
Temperature (˚F)
70
Flow (cfs)
75
ay
Au
g
40
ec
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
80
M
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
Date
85
45
N
45
Date
50
RM 3.7 Noble Ave.
daily max
daily min
50
D
ov
N
ct
O
Se
p
Au
g
l
Ju
Ju
n
M
ay
40
55
l
45
60
Ju
max
min
65
Ju
n
60
70
Temperature (˚F)
65
75
M
Temperature (˚F)
70
80
ay
75
85
Flow (cfs)
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
80
50
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
Date
85
55
O
ec
Date
ct
40
D
ov
N
ct
O
Se
p
Au
g
l
Ju
Ju
n
M
ay
40
50
Se
p
45
daily max
daily min
Se
p
50
55
Au
g
daily max
daily min
l
55
60
Ju
60
65
Ju
n
65
70
M
Temperature (˚F)
70
75
Temperature (˚F)
75
80
ay
80
85
Flow (cfs)
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
85
Flow (cfs)
Appendix A
Flow (cfs)
Date
Stillwater Sciences
A-24
Appendix A
LITERATURE CITED
Abel, J. 2001. “Barrierness”: Qualitatively assessing fish passage impediments.
Unpublished memo to FAHCE Consensus Committee. 17 April.
Abel, J. 2005. Personal communication with Jae Abel of SCVWD (Santa Clara Valley
Watershed District), City of San Jose, California. 11 January.
Barnard, K., and S. McBain. 1994. Standpipe to determine permeability, dissolved oxygen,
and vertical particle size distribution in salmonid spawning gravels. Fish Habitat
Relationships Technical Bulletin No. 15. USDA Forest Service.
Connor, E. J. 1996. Comparative evaluation of Pacific giant salamander and steelhead trout
populations among streams in old-growth and second-growth forests of northwest
California. Ph. D. dissertation. University of California, Davis.
FAHCE (Fisheries and Aquatic Habitat Collaborative Effort). 2000. Summary and
conclusion FAHCE TAC evaluation of the effects of Santa Clara Valley Water District
facilities and operations on factors limiting habitat availability and quality for steelhead
and chinook salmon.
Hankin, D. G., and G. H. Reeves. 1988. Estimating total fish abundance and total habitat
area in small streams based on visual estimation methods. Canadian Journal of Fisheries
and Aquatic Sciences 45:834-844.
Hilton, S., and T. E. Lisle. 1993. Measuring the fraction of pool volume filled with fine
sediment. Research Note PSW-RN-414. USDA Forest Service, Pacific Southwest Research
Station, Berkeley, California.
Kondolf, G. M., and M. G. Wolman. 1993. The sizes of salmonid spawning gravels. Water
Resources Research 29: 2275-2285.
Li, S. K. 2001. Electrofishing surveys on Guadalupe Creek, Stevens Coyote and Penitencia
Creeks: catch results. Prepared by Stacy K. Li with Aquatic Systems Research, for the
FAHCE Technical Advisory Committee.
McCain, M., D. Fuller, L. Decker, and K. Overton. 1990. Stream habitat classification and
inventory procedures for northern California. FHR Currents, Fish Habitat Relationships
Technical Bulletin No. 1. U. S. Forest Service, Pacific Southwest Region, Arcata,
California.
McCuddin, M. E. 1977. Survival of salmon and trout embryos and fry in gravel-sand
mixtures. Master's thesis. Department of University of Idaho, Moscow.
Ricker, W. E. 1976. Review of the rate of growth and mortality of Pacific salmon in salt
water and non-catch mortality caused by fishing. Journal of the Fisheries Research Board
of Canada 33: 1483-1524.
Stillwater Sciences
A-25
Appendix A
Shapovalov, L., and A. C. Taft. 1954. The life histories of the steelhead rainbow trout
(Salmo gairdneri gairdneri) and silver salmon (Oncorhynchus kisutch) with special
reference to Waddell Creek, California, and recommendations regarding their management.
Fish Bulletin. 98. California Department of Fish and Game.
Smith, J. 1997. Personal communication with Heidi Fish regarding steelhead/ rainbow trout
in several Monterey Bay and San Francisco Bay streams. Professor, Department of
Biological Sciences, San Jose State University, San Jose, California. 9 June.
Stillwater Sciences and Dietrich, W.E. 2002. Napa River Basin Limiting Factors Analysis.
Prepared for San Francisco Bay Water Quality Control Board and California State Coastal
Conservancy by Stillwater Sciences, Berkeley, California and W.E. Dietrich, Department
of Earth and Planetary Sciences, University of California, Berkeley. Executive Summary
and Technical Report Text both available online at
http://www.swrcb.ca.gov/~rwqcb2/Download.htm and
http://www.coastalconservancy.ca.gov/Programs/napa.htm
Tagart, J. V. 1976. The survival from egg deposition to emergence of coho salmon in the
Clearwater River, Jefferson County, Washington. Master's thesis. Department of University
of Washington, Seattle.
Terhune, L. D. B. 1958. The Mark VI groundwater standpipe for measuring seepage
through salmon spawning gravel. Journal of the Fisheries Research Board of Canada 15:
1027-1063
Stillwater Sciences
A-26
Appendix B
APPENDIX B:
STEELHEAD SPECIES SUMMARY
Stillwater Sciences
Appendix B
Table of Contents
APPENDIX B
B1.1
B1.2
B1.3
B1.4
B1.5
B1.6
B1.7
B1.8
STEELHEAD SPECIES SUMMARY............................................................ B-1
S TATUS ....................................................................................................................... B-1
G EOGRAPHIC D ISTRIBUTION ......................................................................................... B-1
P OPULATION TRENDS ................................................................................................... B-1
LIFE H ISTORY .............................................................................................................. B-2
A DULT U PSTREAM MIGRATION AND S PAWNING ............................................................ B-2
H ABITAT REQUIREMENTS ............................................................................................. B-6
ECOLOGICAL I NTERACTIONS ........................................................................................ B-8
RESPONSES TO A NTHROPOGENIC W ATERSHED D ISTURBANCES ...................................... B-9
LITERATURE CITED ........................................................................................................... B-25
List of Tables
Table B-1. Adult holding velocity criteria for steelhead. .......................................................... B-12
Table B-2. Adult holding depth criteria for steelhead. ............................................................... B-12
Table B-3. Adult spawning velocity criteria for steelhead......................................................... B-13
Table B-4. Adult spawning depth criteria for steelhead. ........................................................... B-14
Table B-5. Fry early summer rearing velocity criteria for steelhead. ......................................... B-15
Table B-6. Fry early summer rearing depth criteria for steelhead. ............................................. B-16
Table B-7. Age 0+ summer rearing (late summer/fall) velocity criteria for steelhead. ............... B-16
Table B-8. Age 0+ summer rearing (late summer/fall) depth criteria for steelhead. ................... B-18
Table B-9. Age 0+ summer rearing (late summer/fall) for steelhead not related to depth or velocity.
......................................................................................................................................... B-20
Table B-10. Age 0+ winter rearing velocity criteria for steelhead. ............................................ B-20
Table B-11. Age 0+ winter rearing depth criteria for steelhead. ................................................ B-20
Table B-12. Age 0+ winter rearing habitat criteria for steelhead not related to depth or velocity. .....
......................................................................................................................................... B-21
Table B-13. Age 1+ and older summer rearing velocity criteria for steelhead. .......................... B-21
Table B-14. Age 1+ and older summer rearing depth criteria for steelhead. .............................. B-22
Table B-15. Age 1+ and older summer rearing for steelhead not related to depth or velocity..... B-23
Table B-16. Age 1+ and older winter rearing velocity criteria for steelhead. ............................. B-23
Table B-17. Age 1+ and older winter rearing depth criteria for steelhead.................................. B-23
Table B-18. Age 1+ and older rearing velocity criteria for steelhead [SEASON NOT SPECIFIED].
......................................................................................................................................... B-24
Table B-19. Age 1+ and older rearing depth criteria for steelhead [SEASON NOT SPECIFIED]. ....
......................................................................................................................................... B-24
Stillwater Sciences
APPENDIX B
Appendix B
STEELHEAD SPECIES SUMMARY
Common Name: Steelhead
Scientific Name: Oncorhynchus mykiss
Legal Status: Federal Threatened (Central California Coast ESU, listed in 1997 [62 FR
43937])
State
None
B1.1 Status
Two major O. mykiss genetic groups exist in the Pacific Northwest; a coastal and an inland
group, separated by the Cascade Range crest (Schreck et al. 1986, Reisenbichler et al.
1992). Upper Penitencia Creek steelhead belong to the subspecies O. m. irideus, or coastal
rainbow trout and steelhead, that extends east to the Cascades (Behnke 1992). Steelhead
found in Upper Penitencia Creek and the Coyote Creek watershed belong to the Central
California Coast evolutionarily significant unit (ESU) (NMFS 1997) and were designated
as a federally threatened species on August 18, 1997 (NMFS 1997). This ESU extends
from the Russian River to Aptos Creek, and includes tributaries to San Francisco and San
Pablo bays eastward to the Napa River, excluding the Sacramento-San Joaquin River Basin.
Both winter-run steelhead and non-anadromous resident forms of rainbow trout occur in
tributaries to the San Francisco estuary (Leidy et al. 2003).
B1.2 Geographic Distribution
Steelhead are distributed throughout the North Pacific Ocean and historically spawned in
streams along the west coast of North America from Alaska to northern Baja California.
The species is currently known to spawn only as far south as Malibu Creek in southern
California (Barnhart 1991, NMFS 1996a).
B1.3 Population Trends
The National Marine Fisheries Service (NMFS 1996a) has concluded that populations of
naturally reproducing steelhead have been experiencing a long-term decline in abundance
throughout their range. Populations in the southern portion of the range have experienced
the most severe declines, particularly in streams from California's Central Valley and south,
where many stocks have been extirpated (NMFS 1996a). During the 1900s, 23 naturally
reproducing populations of steelhead are believed to have been extirpated in the western
United States. Many more are thought to be in decline in Washington, Oregon, Idaho, and
California. Based on analyses of dam and weir counts, stream surveys, and angler catches,
NMFS (1997) concluded that, of the 160 west coast steelhead stocks for which adequate
data were available, 118 (74%) exhibited declining trends in abundance, while the
remaining 42 (26%) exhibited increasing trends.
Accurate population size estimates are not available for Upper Penitencia Creek or most
other San Francisco Estuary streams due to lack of reliable information (Leidy et al. 2003).
Although historical data on salmonid presence, spawning, and viability is incomplete, it is
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Appendix B
believed existing San Francisco Bay area steelhead runs have declined largely due to
habitat impacts such as artificial barriers, reduction of habitat quantity and quality due to
land use, and water withdrawals (Leidy et al. 2003). On a larger scale, steelhead stocks in
the state of California have declined substantially. The most recently available estimate of
California’s steelhead population is roughly 250,000 adults, which is nearly half the adult
population that existed 30 years ago (McEwan and Jackson 1996). Current estimates of all
steelhead adults returning to San Francisco Bay tributaries combined are well below 10,000
fish (Leidy 2001). Upper Penitencia Creek is one of only a few creeks in the South Bay that
support steelhead runs (Buchan et al. 1999) and has been described as having the best
steelhead habitat (SCBWMI 2003).
B1.4 Life History
Steelhead is the term used to distinguish anadromous populations of rainbow trout from
resident populations. Much life history variability exists among steelhead populations;
however, populations may be broadly categorized into two reproductive groups, most
commonly referred to as either winter-run or summer-run. Steelhead in Upper Penitencia
Creek are all winter-run.
B1.5 Adult Upstream Migration and Spawning
Steelhead return to spawn in their natal stream, usually in their fourth or fifth year of life,
with males typically returning to freshwater earlier than females (Shapovalov and Taft
1954, Behnke 1992). A small percentage of steelhead may stray into streams other than
those in which they originated. Winter-run steelhead generally enter spawning streams
from fall through spring as sexually mature adults and spawn a few months later in late
winter or spring (Roelofs 1985, Meehan and Bjornn 1991, Behnke 1992).
Adult steelhead migrate upstream on both the rising and falling limbs of high flows, but do
not appear to move during flood peaks. Some authors have suggested that increased water
temperatures trigger movement, but some steelhead ascend into freshwater without any
apparent environmental cues (Barnhart 1991). Peak upstream movement appears to occur
in the morning and evening, although steelhead have been observed to move at all hours
(Barnhart 1991). Adult winter steelhead are not believed to feed to any great extent during
their freshwater spawning migration (Shapovalov and Taft 1954). Delays experienced
during migration may therefore affect reproductive success.
Steelhead are among the strongest swimmers of freshwater fishes. Cruising speeds, which
are used for long-distance travel, are up to 5 ft/s (1.5 m/s); sustained speeds, which may
last several minutes and are used to surmount rapids or other barriers, range from 5–15 ft/s
(1.5–4.6 m/s). Darting speeds, which are brief bursts used in feeding and escape, range
from 14–27 ft/s (4.3–8.2 m/s) (Bell 1973, as cited in Everest et al. 1985; Roelofs 1987).
Steelhead have been observed making vertical leaps of up to 17 ft (5.2 m) over falls (W.
Trush per. comm., as cited in Roelofs 1987).
During spawning, female steelhead create depressions in streambed gravels by vigorously
pumping their body and tail horizontally near the streambed. Steelhead redds are
approximately 4–12 in (10–30 cm) deep, 15 in (38-cm) in diameter, and oval in shape
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Appendix B
(Needham and Taft 1934, Shapovalov and Taft 1954). Males do not assist with redd
construction, but may fight with other males to defend spawning females (Shapovalov and
Taft 1954). Males fertilize the female's eggs as they are deposited in the redd, after which
the female moves to the upstream end of the nest and stirs up additional gravel, covering
the egg pocket (Orcutt et al. 1968). Females then move two to three feet upstream and dig
another pit, enlarging the redd. Females may dig six to seven egg pockets, moving
progressively upstream, and spawning may continue for several days to over a week
(Needham and Taft 1934). A female approximately 33 in (85 cm) in length may lay 5,000
to 10,000 eggs, with fecundity being related to age and length of the adult female and
varying between populations (Meehan and Bjornn 1991). A range of 1,000 to 4,500 eggs
per female has been observed within the Sacramento Drainage (Mills and Fisher 1994, as
cited in Leidy 2001). In cases where spawning habitat is limited, late-arriving spawners
may superimpose their redds atop existing nests, resulting in mortality of eggs and alevins
that were in the original redd (Orcutt et al. 1968).
Although most steelhead die after spawning, adults are capable of returning to the ocean
and migrating back upstream to spawn in subsequent years, unlike most other Pacific
salmon. Runs may include from 10 to 30% repeat spawners, the majority of which are
females (Ward and Slaney 1988, Meehan and Bjornn 1991, Behnke 1992). Repeat
spawning is more common in smaller coastal streams than in large drainages requiring a
lengthy migration (Meehan and Bjornn 1991). Hatchery steelhead are typically less likely
than wild fish to survive to spawn a second time (Leider et al. 1986).
Whereas females spawn only once before returning to the sea, males may spend two or
more months in spawning areas and may mate with multiple females, incurring higher
mortality and reducing their chances of repeat spawning (Shapovalov and Taft 1954).
Steelhead may migrate downstream to the ocean immediately following spawning or may
spend several weeks holding in pools before outmigrating (Shapovalov and Taft 1954).
Egg Incubation, Alevin Development, and Fry Emergence
Hatching of eggs follows a 20- to 100-day incubation period, the length of which depends
on water temperature (Shapovalov and Taft 1954, Barnhart 1991). In Waddell Creek (San
Mareo County), Shapovalov and Taft (1954) found incubation times between 25 and 30
days. Newly-hatched steelhead alevins remain in the gravel for an additional 14–35 days
while being nourished by their yolk sac (Barnhart 1991). Fry emerge from the substrate
just before total yolk absorption under optimal conditions; later-emerging fry that have
already absorbed their yolk supply are likely to be weaker (Barnhart 1991). Upon
emergence, fry inhale air at the stream surface to fill their air bladder, absorb the remains
of their yolk, and start to feed actively, often in schools (Barnhart 1991, NMFS 1996b).
Survival from egg to emergent fry is typically less than 50% (Meehan and Bjornn 1991),
but may be quite variable depending upon local conditions.
Juvenile Freshwater Rearing
Juvenile steelhead (parr) rear in freshwater before outmigrating to the ocean as smolts. The
duration of time parr spend in freshwater appears to be related to growth rate, with larger,
faster-growing members of a cohort smolting earlier (Peven et al. 1994). Steelhead in
warmer areas, where feeding and growth are possible throughout the winter, may require a
shorter period in freshwater before smolting, while steelhead in colder, more northern, and
inland streams may require three or four years before smolting (Roelofs 1985).
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Appendix B
Juveniles typically remain in their natal streams for at least their first summer, dispersing
from fry schools and establishing feeding territories (Barnhart 1991). Peak feeding and
freshwater growth rates occur in late spring and early summer. In Steamboat Creek, a
major steelhead spawning tributary in the North Umpqua River watershed, juveniles
typically rest in the interstices of rocky substrate in the morning and evening, and rise into
the water column and orient themselves into the flow to feed during the day when water
temperatures are higher (Dambacher 1991). In the Smith River of Oregon, Reedy (1995)
suggested that rising stream temperatures and reduced food availability occurring in late
summer may lead to a decline in steelhead feeding activity and growth rates.
Juveniles either overwinter in their natal streams if adequate cover exists or disperse as presmolts to other streams to find more suitable winter habitat (Bjornn 1971, Dambacher
1991). As stream temperatures fall below approximately 44.6°F (7°C) in the late fall to
early winter, steelhead enter a period of winter inactivity spent hiding in the substrate or
closely associated with instream cover, during which time growth ceases (Everest and
Chapman 1972). Age 0+ steelhead appear to remain active later into the fall than 1+
steelhead (Everest et al. 1986). Winter hiding behavior of juveniles reduces their
metabolism and food requirements and reduces their exposure to predation and high flows
(Bustard and Narver 1975), although substantial mortality appears to occur in winter,
nonetheless. Winter mortalities ranging from 60 to 86% for 0+ steelhead and from 18 to
60% for 1+ steelhead were reported in Fish Creek in the Clackamas River basin, Oregon
(Everest et al. 1988, as cited in Dambacher 1991).
Juveniles appear to compete for food and rearing habitat with other steelhead. Age 0+ and
1+ steelhead exhibit territorial behavior (Everest and Chapman 1972), although this
behavior may dissipate in winter as fish reduce feeding activity and congregate in suitable
cover habitat (Meehan and Bjornn 1991). Reedy (1995) found that steelhead in the tails of
pools did not exhibit territorialism or form dominance hierarchies.
Parr outmigration appears to be more significant in smaller basins, when compared to
larger basins (Dambacher 1991). In some areas juveniles migrate out of tributaries despite
the fact that downstream rearing habitat may be limited and survival rates low in these
areas, suggesting that migrants are responding to density-related competition for food and
space, or to reduction in habitat quality in tributaries as flows decline (Dambacher 1991,
Peven et al. 1994, Reedy 1995). In relatively small tributaries with good rearing habitat
located downstream, early outmigration may represent an adaptation to improve survival
and may not be driven by environment- or competition-related limitations (Dambacher
1991). Steelhead may overwinter in mainstem reaches, particularly if coarse substrates in
which to seek cover from high flows are available (Reedy 1995), or they may return to
tributaries for the winter (Everest 1973, as cited in Dambacher 1991).
Rearing densities for juvenile steelhead overwintering in high-quality habitats with cobbleboulder substrates are estimated to range from approximately 0.24 fish/ft2 (2.7 fish/m2 ) (W.
Trush, per. comm., 1997) to 0.53 fish/ft2 (5.7 fish/m2 ) (Meyer and Griffith 1997). Everest
and Chapman (1972) report age 0+ densities of 0.12 to 0.14 fish/ft2 (1.3 to 1.5 fish/m2 ) in
preferred habitat in Idaho.
Smolt Outmigration and Estuarine Rearing
At the end of the freshwater rearing period, steelhead migrate downstream to the ocean as
smolts, typically at a length of 5.85 to 7.80 in (15 to 20 cm) (Meehan and Bjornn 1991). A
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Appendix B
length of 5.46 in (14 cm) is typically cited as the minimum size for smolting (Wagner et al.
1963, Peven et al. 1994).
Evidence suggests that photoperiod is the most important environmental variable
stimulating the physiological transformation from parr to smolt (Wagner 1974). During
smoltification, the spots and parr marks characteristic of juvenile coloration are replaced by
a silver and blue-green iridescent body color (Barnhart 1991) and physiological
transformations occur that allow them to survive in salt water.
Less is known regarding the use of estuaries by steelhead than for other anadromous
salmonid species; however, the available evidence shows that steelhead in many systems
use estuaries as rearing habitat. Smith (1990) concluded that even tiny lagoons unsuitable
for summer rearing can contribute to the maintenance of steelhead populations by
providing feeding areas during winter or spring smolt outmigration.
Estuarine rearing may be more important to steelhead populations in the southern half of
the species' range due to greater variability in ocean conditions and paucity of high quality
near-shore habitats in this portion of their range (NMFS 1996a). Estuaries may also be
more important to populations spawning in smaller coastal tributaries due to the more
limited availability of rearing habitat in the headwaters of smaller stream systems (McEwan
and Jackson 1996). Most marine mortality of steelhead occurs soon after they enter the
ocean and predation is believed to be the primary cause of this mortality (Pearcy 1992, as
cited in McEwan and Jackson 1996). Because predation mortality and fish size are likely
to be inversely related (Pearcy 1992, as cited in McEwan and Jackson 1996), the growth
that takes place in estuaries may be very important for increasing the odds of marine
survival (Pearcy 1992, as cited in McEwan and Jackson 1996; Simenstad et al. 1982, as
cited in NMFS 1996a; Shapovalov and Taft 1954).
Steelhead have variable life histories and may migrate downstream to estuaries as age 0+
juveniles or may rear in streams up to four years before outmigrating to the estuary and
ocean (Shapovalov and Taft 1954). Steelhead migrating downstream as juveniles may rear
for one to six months in the estuary before entering the ocean (Barnhart 1991). Shapovalov
and Taft (1954) conducted exhaustive life history studies of steelhead and coho salmon in
Waddell Creek (Santa Cruz County, California) and found that coho salmon went to sea
almost immediately after migrating downstream, but that some of the steelhead remained
for a whole season in Waddell Creek lagoon or the lower portions of the stream before
moving out to sea. Some steelhead individuals remained in the lagoon rather than moving
out to sea and migrated back upstream and underwent a second downstream migration the
following year. In Scott Creek lagoon (Santa Cruz County), Marston (1992, as cited in
McEwan and Jackson 1996) found that half of the steelhead rearing in the lagoon in June
and July of 1992 were less than 90 mm and appeared to be pre-smolts. Coots (1973, as
cited in McEwan and Jackson 1996) found that 34% of juvenile steelhead in San Gregorio
Creek lagoon captured in summer were juveniles less than 3.9 in [100 mm] in length. From
these studies and others, it has been shown estuaries provide valuable rearing habitat to
juvenile and yearling steelhead and not merely a corridor for smolts outmigrating to the
ocean.
Ocean Phase
The majority of steelhead spend one to three years in the ocean, with smaller smolts
tending to remain in salt water for a longer period than larger smolts (Chapman 1958,
Behnke 1992). Larger smolts have been observed to experience higher ocean survival rates
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Appendix B
(Ward and Slaney 1988). Steelhead grow rapidly in the ocean compared to in freshwater
rearing habitats, with growth rates potentially exceeding 0.98 in (2.5 cm) per month
(Shapovalov and Taft 1954, Barnhart 1991). Steelhead staying in the ocean for two years
typically weigh 7 to10 lbs (3.15 to 4.50 kg) upon return to fresh water (Roelofs 1985).
Unlike other salmonids, steelhead do not appear to form schools in the ocean. Steelhead in
the southern part of the species' range appear to migrate close to the continental shelf,
while more northern populations of steelhead may migrate throughout the northern Pacific
Ocean (Barnhart 1991).
B1.6 Habitat Requirements
Adult Upstream Migration and Spawning
During their upstream migration, adult steelhead require deep pools for resting and holding
(Puckett 1975, Roelofs 1983, as cited in Moyle et al. 1989). Deep pool habitat (>4.88 ft
[>1.5 m]) is preferred by summer steelhead during the summer holding period. Steelhead
need water with a minimum depth of 0.59 ft (18 cm) and maximum velocity of 8 ft/s (240
cm/s) for successful upstream migration (Thompson 1972, as cited in Everest et al. 1985).
Relatively cool water temperatures (between 50 and 59°F [10o and 15°C]) are preferred by
adults, although they may survive temperatures as high as 80.6°F (27°C) for short periods
(Moyle et al. 1989). Adult holding habitat requirements for steelhead are shown in Tables
B2-1 and B2-2.
Areas of the stream with water depths from about 7–53 in (18 to 137 cm) and velocities
from 1.97–3.77 ft/s (0.6 to 1.15 m/s) are typically preferred for spawning by adult steelhead
(Moyle et al. 1989, Barnhart 1991). Pool tailouts or heads of riffles with well-oxygenated
gravels are often selected as redd locations (Shapovalov and Taft 1954). The average area
encompassed by a redd is 47–65.56 ft2 (4.4–5.9 m2 ) (Orcutt et al. 1968, Hunter 1973, as
cited in Bjornn and Reiser 1991). Gravels ranging in size from 0.25 to 5.07 in (0.64 to 13
cm) in diameter are suitable for redd construction (Barnhart 1991). Steelhead pairs have
been observed spawning within 3.94 ft (1.2 m) of each other (Orcutt et al. 1968). Bell
(1986) indicates that preferred temperatures for steelhead spawning range from 39.0o to
48.9o F (3.9o to 9.4o C). Steelhead may spawn in intermittent streams, but juveniles soon
move to perennial streams after hatching (Moyle et al. 1989). In the Rogue River drainage,
summer steelhead are more likely to spawn in intermittent streams, while winter steelhead
typically spawn in permanent streams (Roelofs 1985). Spawning habitat requirements for
steelhead are shown in Tables B2-3 and B2-4.
Egg Incubation, Alevin Development, and Fry Emergence
Incubating eggs require dissolved oxygen concentrations, with optimal concentrations at or
near saturation. Low dissolved oxygen increases the length of the incubation period and
cause emergent fry to be smaller and weaker. Dissolved oxygen levels remaining below 2
ppm result in egg mortality (Barnhart 1991). Information available in the literature
indicates that preferred incubation temperatures range from 48.2 to 51.8°F (9 to 11°C)
(McEwan and Jackson 1996, FERC 1993).
Juvenile Freshwater Rearing
Age 0+. After emergence from spawning gravels in spring or early summer, steelhead fry
move to shallow-water, low-velocity habitats such as stream margins and low-gradient
riffles and will forage in open areas lacking instream cover (Hartman 1965, Everest et al.
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Appendix B
1986, Fontaine 1988). As fry increase in size in late summer and fall, they increasingly use
areas with cover and show a preference for higher-velocity, deeper mid-channel waters near
the thalweg (Hartman 1965, Everest and Chapman 1972, Fontaine 1988). In general, age
0+ steelhead occur in a wide range of hydraulic conditions (Bisson et al. 1988), appearing
to prefer water less than 19.5 in (50 cm) deep with velocities below 0.98 ft/s (0.3 m/s)
(Everest and Chapman 1972). Age 0+ steelhead have been found to be relatively abundant
in backwater pools and often live in the downstream ends of pools in late summer (Bisson
et al. 1988, Fontaine 1988). Age 0+ rearing habitat requirements are shown in Tables 5–
12.
Age 1+ and older juveniles. Older age classes of juvenile steelhead (age 1+ and older)
occupy a wide range of hydraulic conditions. They prefer deeper water during the summer
and have been observed to use deep pools near the thalweg with ample cover as well as
higher-velocity rapid and cascade habitats (Bisson et al. 1982, Bisson et al. 1988). Age 1+
fish typically feed in pools, especially scour and plunge pools, resting and finding escape
cover in the interstices of boulders and boulder-log clusters (Fontaine 1988, Bisson et al.
1988). During summer, steelhead parr appear to prefer habitats with rocky substrates,
overhead cover, and low light intensities (Hartman 1965, Facchin and Slaney 1977, Ward
and Slaney 1979, Fausch 1993). Age 1+ steelhead appear to avoid secondary channel and
dammed pools, glides, and low-gradient riffles with mean depths less than 7.8 in (20 cm)
(Fontaine 1988, Bisson et al. 1988, Dambacher 1991).
As steelhead grow larger, they tend to prefer microhabitats with deeper water and higher
velocity as locations for focal points, attempting to find areas with an optimal balance of
food supply versus energy expenditure, such as velocity refuge positions associated with
boulders or other large roughness elements close to swift current with high
macroinvertebrate drift rates (Everest and Chapman 1972, Bisson et al. 1988, Fausch
1993). Reedy (1995) indicates that 1+ steelhead especially prefer high-velocity pool heads,
where food resources are abundant, and pool tails, which provide optimal feeding
conditions in summer due to lower energy expenditure requirements than the more
turbulent pool heads. Fast, deep water, in addition to optimizing feeding versus energy
expenditure, provides greater protection from avian and terrestrial predators (Everest and
Chapman 1972).
Age 1+ steelhead appear to prefer rearing habitats with velocities ranging from 0.33–0.98
ft/s (10–30 cm/s) and depths ranging from 19.5–29.3 in (50–75 cm) (Everest and Chapman
1972, Hanson 1977, as cited in Bjornn and Reiser 1991). During the juvenile rearing
period, steelhead are often observed using habitats with swifter water velocities and
shallower depths than coho salmon (Sullivan 1986, Bisson et al. 1988), a species they are
often sympatric with. In comparison with juvenile coho, steelhead have a fusiform body
shape that is better adapted to holding and feeding in swifter currents (Bisson et al. 1988).
Where the two species coexist, this generally results in spatial segregation of rearing
habitat that becomes most apparent during the summer months. While juvenile coho
salmon are strongly associated with low-velocity habitats such as pools throughout the
rearing period (Shirvell 1990), steelhead will use riffles (age 0+) and higher velocity pool
habitats (age 1+) such as scour and plunge pools in the summer (Sullivan 1986, Bisson et
al. 1982). Habitat requirements of age 1+ and older steelhead are shown in Tables 13–19.
Preferred rearing temperatures range from 45.0 to 57.9°F (7.2 to 14.4°C), with optimum
temperature for juveniles occurring from 50–55.0°F (10–12.8°C) and lethal temperatures
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Appendix B
occurring at 74.8°F (23.8°C) (Bell 1991). Preferred outmigration temperatures are <57°F
(<13°C).
Winter Habitat
Steelhead overwinter in pools, especially low-velocity deep pools with large rocky
substrate or woody debris for cover, including backwater and dammed pools (Hartman
1965, Swales et al. 1986, Raleigh et al. 1984, Fontaine 1988). Juveniles are known to use
the interstices between substrate particles as overwintering cover. Bustard and Narver
(1975) typically found age 0+ steelhead using 3.9–9.7 in (10–25 cm) diameter cobble
substrates in shallow, low-velocity areas near the stream margin. Everest et al. (1986)
observed age 1+ steelhead using logs, rootwads, and interstices between assemblages of
large boulders (39.0 in [>100 cm] diameter) surrounded by small boulder to cobble size
(19.7–39.0 in [50–100 cm] diameter) materials as winter cover. Age 1+ fish typically stay
within the area of the streambed that remains inundated at summer low flows, while age 0+
fish frequently overwinter beyond the summer low flow perimeter along the stream margins
(Everest et al. 1986).
In winter, 1+ steelhead prefer water deeper than 17.5 in (45 cm), while age 0+ steelhead
often occupy water less than 5.8 in (15 cm) deep and are rarely found at depths over about
23.4 in (60 cm) (Bustard and Narver 1975). Below 44.6o F (7 o C), juvenile steelhead prefer
water velocities 0.5 ft/s (<15 cm/s) (Bustard and Narver 1975). Spatial segregation of
stream habitat by juvenile coho salmon and steelhead is less pronounced in winter than in
summer, although older juvenile steelhead may prefer deeper pools than coho salmon
(Bustard and Narver 1975). Overwinter habitat requirements of juvenile steelhead are
shown in Tables B10–12, and in Tables B16–17.
Ocean Phase
Little is known about steelhead use of ocean habitat, although changes in ocean conditions
are important for explaining trends among Oregon coastal steelhead populations (Kostow
1995). Evidence suggests that increased ocean temperatures associated with El Niño events
may increase ocean survival as much as two-fold (Ward and Slaney 1988). The magnitude
of upwelling, which determines the amount of nutrients brought to the ocean surface and
which is related to wind patterns, influences ocean productivity with significant effects on
steelhead growth and survival (Barnhart 1991). Steelhead appear to prefer ocean
temperatures of 48.2o–52.7o F (9 o–11.5o C) and typically swim in the upper 30–40 ft (9–12
m) of the ocean's surface (Barnhart 1991).
B1.7 Ecological Interactions
Food Web Interactions
Emergent fry initially feed on zooplankton and other microorganisms (Barnhart 1991).
Juveniles feed on a wide range of items, primarily those associated with the stream bottom
such as aquatic insects, amphipods, aquatic worms, fish eggs, and occasionally smaller fish
(Wydoski and Whitney 1979). Juveniles may also feed on spiders, mollusks, and fish,
including smaller steelhead (Roelofs 1985). Age 0+ steelhead prefer benthic invertebrates
(Johnson and Ringler 1980); larger steelhead, having larger mouths, can consume a broader
range of foods (Fausch 1991). In the ocean, steelhead feed on juvenile greenling, squids,
amphipods, and other organisms (Barnhart 1991).
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Appendix B
Adult summer steelhead apparently do not usually feed in fresh water and can endure long
periods without food, during which time their stomachs shrink (Shapovalov and Taft 1954,
Roelofs 1987). Summer steelhead, which spend longer periods in fresh water before
spawning, may be more likely to feed in freshwater than adult winter steelhead. Food
items taken by adults include caddisflies, mayflies, stoneflies, salmon eggs and,
infrequently, other fish (Barnhart 1991).
Major predators of adult steelhead include humans, marine mammals, and large pelagic
fish. Eggs may be eaten by macroinvertebrates, crayfish, and other fish. Juvenile steelhead
may be preyed upon by garter snakes, piscivorous fish such as older salmonids (including
steelhead), freshwater sculpins, introduced piscivorous fish (e.g., smallmouth bass, striped
bass), mammals (e.g., river otter, mink), and piscivorous birds (e.g., mergansers,
kingfishers, herons, ospreys, loons). Juvenile steelhead have been observed feeding on
emergent fry (Shapovalov and Taft 1954).
B1.8 Responses to Anthropogenic Watershed Disturbances
An anadromous life history and changes in habitat requirements at different life stages
make steelhead vulnerable to a wide range of watershed disturbances, including dams,
timber harvest, road construction, recreational use, and other human-related disturbances.
The relative importance of anthropogenic and natural disturbances and of ocean conditions
for controlling steelhead populations is uncertain. Coastal steelhead habitats, which
historically consisted of old-growth temperate moist conifer forests with streams having
high structural complexity, have been significantly altered (Kostow 1995).
Physical Barriers to Migration and Movement
Dams without fish passage facilities block migration to historically available spawning
and/or rearing areas, inundate spawning and rearing habitat beneath reservoirs, and alter
hydrologic regimes, sediment and LWD budgets, water temperatures, nutrient cycling, and
food supplies (Collins 1976). Where fish passage facilities are provided at dams, delays to
upstream or downstream migration may occur, and stress, injury, or mortality may result
from passage through juvenile bypass facilities.
Two natural waterfalls, one in Upper Penitencia Creek and one in Arroyo Aguague, are
complete barriers to upstream migration (FAHCE 2000). Although several partial structural
barriers (impediments) exist in Coyote Creek and Upper Penitencia Creek (FAHCE 2000),
the passage assessment conducted by Stillwater Sciences for this study indicates that
spawning adults likely have unimpeded upstream access to the waterfalls during most
winter and spring flow conditions. In downstream reaches, however, water diversions and
potentially warm water temperatures may reduce passage opportunities for outmigrating
smolts. The extent to which this occurs, however, could not be determined with available
data.
Stillwater Sciences
B-9
Appendix B
Changes to Hydrologic Regimes
Changes to natural flow regimes may impact steelhead populations through changes to
stimuli used for timing of upstream and downstream migrations, dewatering of redds,
displacement of fry or juveniles, scouring of spawning gravels, and changes to the quality
and quantity of habitat for different life stages. Rapid decreases in flow associated with
hydroelectric project operations may cause stranding, especially of recently emerged fry
because of their preference for stream margin areas of mainstem channels and because they
are relatively weak swimmers (Hunter 1992). Vulnerability to stranding declines once
juvenile steelhead reach lengths of 1.8 inches (45 mm) (R.W. Beck and Associates 1987).
As juveniles grow, they are more likely to occupy deeper areas further from channel
margins, reducing their susceptibility to stranding. Flow diversions may delay or stop adult
migration if minimum water depths are not maintained (Everest et al. 1985).
Changes to Sediment Dynamics
Sedimentation of streams resulting from increased erosion may reduce spawning success of
steelhead and the carrying capacity of juvenile rearing areas. Sedimentation due to land
use activities has been recognized as a primary cause of habitat degradation for steelhead
populations on the west coast (NMFS 1996a). Increased input of fine sediment resulting
from natural or anthropogenic disturbance may be the principle cause of egg and alevin
mortality in some areas (Shapovalov and Taft 1954). Filling of interstitial spaces with fine
sediments reduces intragravel flow through redds, reducing dissolved oxygen
concentrations and the rate of removal of metabolic wastes (Everest et al. 1985). Alevins
that develop in oxygen-deficient gravels are smaller at emergence, placing them at a
competitive disadvantage (Doudoroff and Warren 1965, as cited in Everest et al. 1985).
Interstitial habitat used as cover by juvenile steelhead is also reduced if embedded in fine
sediments. Bjornn et al. (1977) observed reduced juvenile steelhead abundance in Idaho
streams characterized by a high degree of substrate embeddedness.
Accumulation of fine organic material in gravel, which may occur following logging or
other land use disturbances, can also reduce the amount of dissolved oxygen available to
incubating eggs, since the decay of this material consumes oxygen (Barnhart 1991).
Filling of pools with fine sediments can reduce carrying capacity of rearing habitats for
juvenile salmonids (Bjornn et al. 1977). Sedimentation also fills interstitial spaces in the
substrate that are used as velocity refuges by juvenile salmonids during high-flow events or
low temperatures (Hillman et al. 1987) and may reduce aquatic invertebrate production and
therefore reduce juvenile salmonid production (Crouse et al. 1981).
Reductions of bedload supply and/or changes in bed stability are downstream geomorphic
effects often associated with dams (Williams and Wolman 1984, Ligon et al. 1995).
Bedload is that portion of the sediment load carried by rivers that consists of larger
particles, including spawning gravels, that are pushed along or near the bed, as opposed to
suspended load (Leopold 1994). Dams can reduce spawning gravel availability in
downstream reaches and cause development of a coarse, relatively immobile surface layer.
Dams can cause a number of changes to channel morphology or fluvial processes that can
have deleterious effects on stream and riparian habitats, including channel incision and/or
widening, increased bank erosion, and reduced channel migration (Ligon et al. 1995).
Stillwater Sciences
B-10
Appendix B
Changes to Large Woody Debris Dynamics
Reductions in the amount of LWD in stream channels due to either past removal (stream
cleaning) efforts or harvest of streamside trees may reduce the carrying capacity of these
streams for juvenile anadromous salmonids, especially of the older age classes which may
prefer deeper habitats, and may reduce the occurrence of deep pools used by adults during
migration and holding (NMFS 1996a). Murphy et al. (1985, 1986) found that higher
juvenile steelhead densities occurred in reaches with buffer strips adjacent to clearcuts than
in reaches without buffer strips where LWD had been removed. Reduced LWD may also
result in decreased retention of spawning gravels and of fine and coarse particulate organic
matter and salmonid carcasses important for nutrient cycling and maintenance of
macroinvertebrate communities.
Changes to Stream Temperatures and Water Quality
Factors that result in increased stream temperatures, such as large-scale clearcutting,
removal of riparian vegetation, and changes to natural flow regimes may reduce steelhead
populations both directly through increased mortality and indirectly through such factors as
changes to growth rates or timing of emergence and downstream migration.
Warm water temperatures may favor competitors of juvenile steelhead, such as redside
shiners (Reeves et al. 1987). Increases in water temperatures may also make juvenile
anadromous salmonids more susceptible to mortality from diseases such as Flexibacter
columnaris (Holt et al. 1975).
Reservoirs
Reservoir conditions can adversely affect anadromous fish populations. Reservoirs
submerge spawning and rearing habitat, and juvenile anadromous fish traveling
downstream through reservoirs may be subject to mortality through entrainment and
predation by introduced or native fish species in these areas. Reservoir characteristics,
including reduced water velocities, thermal stratification, and low dissolved oxygen levels
may delay downstream migration and extend the exposure of smolts to disease and
predation risks (Collins 1976, Spence et al. 1996).
Poaching and Other Impacts on Adult Holding Habitat
Summer steelhead adults are vulnerable to human disturbance during their holding period.
Holding steelhead are vulnerable to poaching, because they typically congregate in large
numbers in a relatively small number of suitable pools. Steelhead fishing has been
restricted in many areas in response to population declines, but the species remains
vulnerable to poaching. Adult summer steelhead are especially vulnerable to poaching
during summer low flows. Roelofs (1983, as cited by Moyle et al. 1989) has indicated that
steelhead populations showing signs of severe declines tend to be in areas that are more
accessible to people, while stable populations tend to be found in the most inaccessible
streams. Poachers may capture adult steelhead by snagging, spearing, netting, trapping,
shooting, or blasting (Roelofs 1987).
In both tributaries and the mainstem, increased human disturbance associated with
recreational activities such as boating, swimming, or fishing may affect adult holding
habitat; Moyle et al. (1989) indicate that these types of activities may stress adult fish and
result in increased mortality in streams heavily used for recreation. These impacts would
not affect winter steelhead, which do not require extended use of holding areas prior to
spawning.
Stillwater Sciences
B-11
Appendix B
Estuary Impacts
Estuary conditions may have an important influence on anadromous fish survival, since
anadromous fish must pass through these areas during upstream and downstream migration
and since estuarine rearing prior to ocean entry is a life history strategy used by many
juvenile anadromous fish to increase marine survival (Giger 1972, Healey 1991, McMahon
and Holtby 1992). Degradation of estuary habitats due to diking and filling, increased
temperatures, introduction of piscivorous fish, sedimentation due to upstream impacts, and
other human activities may have contributed to anadromous fish declines in California and
in Upper Penitencia Creek.
Table B-1. Adult holding velocity criteria for steelhead.
VELOCITY CRITERIA
minimum
maximum
average
SOURCE
preferred/
optimal
2.44 m/s
(8.01 ft/s)
28.6 cm/s
(0.94 ft/s)
NOTES
(e.g., methods, presence of other
species, complicating factors)
Thompson (1972) as
cited in Bjornn and
Reiser (1991)
Race not specified.
Moyle and Baltz (1985)
as cited in Spence
(1996)
Race not specified, methods not
stated.
Table B-2. Adult holding depth criteria for steelhead.
DEPTH CRITERIA
minimum
maximum
average
SOURCE
preferred/
optimal
NOTES
0.24 m (9.36
in)
Thompson (1972) as
cited in Bjornn and
Reiser (1991)
Race not specified.
300 cm (117
in)
Puckett (1975), Roelofs
(1983) as cited in Moyle
et al. (1989)
Race not specified.
Moyle and Baltz (1985)
as cited in Spence
(1996)
Race not specified, methods not
stated.
82 cm (31.98
(in)
Stillwater Sciences
B-12
Appendix B
Table B-3. Adult spawning velocity criteria for steelhead.
VELOCITY CRITERIA
minimum
maximum
average
SOURCE
preferred/
optimal
NOTES
SUMMER STEELHEAD
23Β155
cm/s
(0.75Β5.09
ft/s)
Cited in Moyle et
al. (1989)
Source of data not provided.
0.431 m/s
(1.41 ft/s)
0.915 m/s
(3.00 ft/s)
0.683 m/s
∀ 0.4823
(2.24 ft/s
∀1.58)
Smith (1973)
Based on 90 redds in the Deschutes River,
Oregon. Velocities were measured at 0.12
m depth over undisturbed gravel just
above the upstream edge of the redd and
were recorded to nearest 0.01 ft/s.
Velocity criteria were defined as the twosided tolerance limits within which there
was 95% confidence that 80% of the
measurements would occur with a normal
distribution.
0.488 m/s
(1.60 ft/s)
0.909 m/s
(2.98 ft/s)
0.698 m/s
∀ 0.4423
(2.29 ft/s
∀ 1.45)
Smith (1973)
Based on 46 redds in the Rouge River
system, Oregon. Velocities were
measured at 0.12 m depth over
undisturbed gravel just above the
upstream edge of the redd and were
recorded to nearest 0.01 ft/s. Velocity
criteria were defined as the two-sided
tolerance limits within which there was
95% confidence that 80% of the
distribution.
Bovee (1978)
50% probability. Based on probability of
use criteria, source of data is not clear.
WINTER STEELHEAD
1.41Β2.85
ft/s (43Β87
cm/s)
0.387 m/s
(1.27 ft/s)
0.869 m/s
(2.85 ft/s)
0.628 m/s
∀0.5455
(2.06 ft/s
∀ 1.79)
Smith (1973)
Based on 113 redds in 11 Oregon streams.
Velocities were measured at 0.12 m depth
over undisturbed gravel just above the
recorded to nearest 0.01 ft/s. Velocity
distribution.
0.387 m/s
(1.27 ft/s)
0.909 m/s
(2.98 ft/s)
0.648 m/s
∀ 0.5472
(2.13 ft/s
∀ 1.80)
Sams and
Pearson (1963)
as cited in Smith
1973)
Based on 49 redds in 2 western Oregon
streams. Velocity values = mean water
column velocity over redds. Velocity
distribution.
1.5 ft/s
(45.73
cm/s)
2.5 ft/s
(76.22
cm/s)
2.2 ft/s
(67.07
cm/s)
Briggs (1953)
Range and average of velocities observed
over 13 redds in Prairie Creek and
Godwood Creek, California.
Stillwater Sciences
B-13
Appendix B
VELOCITY CRITERIA
minimum
maximum
average
SOURCE
NOTES
Carroll (1984) as
cited in Barnhart
(1991)
Not annotated. Range observed in a small
tributary to the Klamath River.
Orcutt et al.
(1968) as cited in
Smith (1973)
Average velocities taken at 0.4 ft (12 cm)
above 54 redds in Idaho.
30Β91
cm/s
(0.98Β2.99
ft/s)
Stober and
Graybill (1974)
as cited in
Spence et al.
(1996)
80% probability
37Β109
cm/s
(1.21Β3.58
ft/s)
Hunter (1973) as
cited in Spence
et al. (1996)
46Β91
cm/s
(21.51Β2.9
9 ft/s)
Graybill et al.
(1979) as cited in
Spence et al.
(1996)
preferred/
optimal
15Β54
cm/s
(0.49Β1.77
ft/s)
2.3Β2.5
ft/s (70Β76
cm/s)
80% probability
Table B-4. Adult spawning depth criteria for steelhead.
DEPTH CRITERIA
minimum
maximum
average
SOURCE
NOTES
Smith (1973)
Based on 83 redds in the Deschutes
River, Oregon. Depths were measured
over undisturbed gravel just above the
recorded to nearest 0.1 ft. Minimum
depth was the limit above which 80% of
measurements could be expected to
occur with 95% confidence.
preferred/
optimal
SUMMER STEELHEAD
0.244 m
(9.52 in)
0.406 m ∀
0.4756
(15.83 in
∀18.55)
10Β150 cm
(3.9Β58.5
in)
Cited in Moyle
et al. (1989)
0.78Β1.79
ft
(23.78Β54.5
7 cm)
Bovee (1978)
Source of data not provided.
WINTER STEELHEAD
50% probability. Source of data is not
clear.
Stillwater Sciences
B-14
Appendix B
DEPTH CRITERIA
minimum
maximum
SOURCE
NOTES
preferred/
optimal
average
0.061 m
(2.38 in)
0.417 m
∀0.3325
(16.26 in ∀
12.97)
Smith (1973)
Based on 113 redds in 11 Oregon
streams. Depths were measured over
0.244 m
(9.52 in)
0.386 m ∀
0.4639
(15.05 in ∀
18.09)
Sams and
Pearson (1963,
as cited in
Smith 1973)
Based on 49 redds in 2 western Oregon
streams. Depths were measured over
10.1 in
(25.90 cm)
Briggs (1953)
Range and average of water depths taken
at 13 redds in Prairie and Godwood
creeks in California.
12Β29 cm
(4.68Β11.31
in)
Carroll (1984)
as cited in
Barnhart
(1991)
Not annotated. Range measured over
redds in a Klamath River tributary.
18 cm (7.02
in)
Stober and
Graybill
(1974) as cited
in Spence et
al. (1996)
80% probability
12Β70 cm
(4.68Β27.30
in)
Hunter (1973)
as cited in
Spence et al.
(1996)
27Β88 cm
(10.53Β34.3
2 in)
Graybill et al.
(1979) as cited
in Spence et
al. (1996)
80% probability
Orcutt et al.
(1968) as cited
in Smith
(1973)
Depths taken above 54 redds in Idaho.
7 in (17.95
cm)
14 in (35.90
cm)
0.7 ft (21
cm)
Table B-5. Fry early summer rearing velocity criteria for steelhead.
VELOCITY CRITERIA
minimum
maximum
average
5.2 cm/s
∀7.6
(0.17
ft/s∀0.25
)
preferred/
optimal
LIFE STAGE
NOTES
(e.g., fish size,
season)
Emergent fry,
33.2 mm (1.33
in) FL (n=240)
SOURCE
Shirvell (1990)
NOTES
Mean values for six samples
during altered flows using
reservoir releases; artificially
placed rootwads.
Stillwater Sciences
B-15
Appendix B
Table B-6. Fry early summer rearing depth criteria for steelhead.
DEPTH CRITERIA
minimum
maximum
average
preferred/
optimal
38.1 cm
∀4.3
(14.86 in
∀1.68)
LIFE STAGE
NOTES
(e.g., fish size,
season)
SOURCE
Emergent fry,
33.2 mm (1.33
in) FL (n=240)
Shirvell (1990)
NOTES
Mean values for six samples
during altered flows using
reservoir releases; artificially
placed rootwads.
Table B-7. Age 0+ summer rearing (late summer/fall) velocity criteria for steelhead.
VELOCITY CRITERIA
minimum
maximum
average
preferred/
optimal
<15 cm/s
(0.49 ft/s)
Highest densities of juvenile fish
observed in a range of habitat
characteristics.
Early summer.
35.6 mm
(1.42 in) FL.
Bugert et al.
(1991)
Not annotated. Bankside and
snorkel observations of fish
habitat use.
Age 0.
Season not
stated
Moyle and Baltz
(1985) as cited
in Spence et al.
(1996)
Methods not stated.
32.4 mm
(1.30 in) total
length
Stuehrenberg
(1975)
Measured the densities of fish
using a range of habitat
characteristics.
6Β49 cm/s
(0.20Β1.61
ft/s)
Age 0.
Season not
stated.
Thompson
(1972) as cited
in Spence et al.
(1996)
Methods not stated.
40 cm/s
(1.31 ft/s)
Fish
length=31Β44
mm
(1.24Β1.76
in). Season
not stated.
Bugert (1985) as
cited Spence et
al. (1996)
Methods not stated.
66Β86 %
occupied
<20 cm/s in
both
seasons
Summer.
Average total
length 64.2
mm
Johnson and
Kucera (1985)
Observations were made on the
habitat utilization of 801 age 0+
steelhead in three Clearwater
River tributaries, Idaho. Also
examined available habitat.
Bedrock Creek
0.46 ft/s
(14 cm/s)
12.4 cm/s
∀ 10.4
(4.8 in ∀
4.1)
NOTES
Everest and
Chapman (1972)
7.3 cm/s
(0.24 ft/s)
0.85 ft/s
(26 cm/s)
SOURCE
Emergent fry
about 32 mm
FL.
21.2 cm/s
∀ 2.99
(0.70 ft/s
∀0.10)
0.10 ft/s (3
cm/s)
LIFE STAGE
NOTES
(e.g., fish
size, season)
18.1 cm/s
∀17.4 (7.1
in ∀ 6.8)
Big Canyon Creek
Stillwater Sciences
B-16
Appendix B
VELOCITY CRITERIA
minimum
maximum
average
preferred/
optimal
LIFE STAGE
NOTES
(e.g., fish
size, season)
SOURCE
16.6 cm/s
∀12.3 (6.5
in ∀ 4.8)
NOTES
Cottonwood Creek
12.5 cm/s
∀ 12.0
(4.9 in ∀
4.7)
Autumn.
Average total
length 84.5
mm
Johnson and
Kucera (1985)
Methods; see above
Bedrock Creek
12.1 cm/s
∀ 12.3
(4.7 in ∀
4.8)
Big Canyon Creek
14.2 cm/s
∀ 11.4
(5.5 in ∀
4.4)
Cottonwood Creek
Approx.
range 1Β6
cm/s
(0.03Β0.20
ft/s)
Total length
2.5 cm (0.98
in)
Late April and
early May
Smith and Li
(1983)
Focal point velocities measured at
locations where fish were
observed using direct observation
in Vas Creek, California. Fish
were then electrofished to obtain
length data. Relative habitat
availability was also determined.
Α...steelhead selected focal points
where water velocities were higher
than those typically available in
Vas Creek...our results probably
underestimate mean water
velocities at focal points...≅
Invertebrate drift increased with
water velocity. Data in this form
is approximated from Figure 2 on
page 176 of Smith and Li (1983).
Approx.
range 5Β10
cm/s
(0.16Β0.33
ft/s)
Total length 5
cm (1.95 in)
Late April and
early May
Smith and Li
(1983)
Methods, see above.
Approx.
range
11Β30 cm/s
(0.36Β0.98
ft/s)
Total length
7.5 cm (2.93
in) September
to December
Smith and Li
(1983)
Methods, see above.
0.40Β0.80
ft/s
(12.20Β24.
39 cm/s)
June
sampling;
total length
ranged 32Β46
mm
(1.28Β1.84
in); average
total length =
36.5 mm
(1.46 in)
Sheppard and
Johnson (1985)
Methods included both direct
observations of fish focal points
and seining of very small areas.
Values are for mean current
velocities. Tributaries to Lake
Ontario, New York, with juvenile
coho present. Range in which fish
Αpredominantly occurred.≅ N=20.
Summer flows were approximately
15Β20 cfs (0.42Β0.57 ft 3 /s). ΑThe
utilization of areas with higher
current velocities in June may
reflect the actual physical
Stillwater Sciences
B-17
Appendix B
VELOCITY CRITERIA
minimum
maximum
average
preferred/
optimal
LIFE STAGE
NOTES
(e.g., fish
size, season)
SOURCE
NOTES
characteristics of the streams
rather than behavioral preferences
of these species because stream
discharge, and hence, mean
current velocities were higher
during the June sampling period.≅
0.10Β0.80
ft/s
(3.05Β24.3
9 cm/s)
October
sampling;
total length
ranged 51Β86
mm
(2.04Β3.44
in); average
total length =
67.1 mm
(2.68 in)
Sheppard and
Johnson (1985)
steelhead present. Range in which
fish Αpredominantly occurred.≅
Flows in October were 60Β70%
lower than in June. N=42.
Table B-8. Age 0+ summer rearing (late summer/fall) depth criteria for steelhead.
DEPTH CRITERIA
minimum
maximum
average
preferred/
optimal
<15 cm
(5.85 in)
LIFE STAGE
NOTES
(e.g., fish
size, season)
SOURCE
NOTES
Emergent fry
about 32 mm
FL.
Everest and
Chapman (1972)
characteristics.
11.7 cm
∀0.63 (4.56
in ∀ 0.25)
Early summer.
35.6 mm
(1.42 in) FL.
Bugert et al.
(1991)
Not annotated. Bankside and
snorkel observations of fish
habitat use.
35 cm
(13.65 in)
Age 0, season
not stated
Moyle and Baltz
(1985) as cited
in Spence et al.
(1996)
Methods not stated.
<12 in
(30.77 cm)
32.4 mm
(1.30 in) total
length
Stuehrenberg
(1975)
characteristics.
18Β67 cm
(7.02Β26.1
3 in)
Age 0, season
not stated.
Thompson
(1972)
Methods not stated.
24 cm (9.36
in)
Fish
length=31Β44
mm
(1.24Β1.76
in). Season
not stated.
Bugert (1985) as
cited Spence et
al. (1996)
Methods not stated.
Stillwater Sciences
B-18
Appendix B
DEPTH CRITERIA
minimum
maximum
average
40 cm
(15.6 in)
(<7% of
observatio
ns > than
40 cm)
Both
seasons
13.6 cm ∀
8.0 (5.3 in
∀3.1)
preferred/
optimal
5Β25 cm
(1.95Β7.80
in) Both
Seasons
LIFE STAGE
NOTES
(e.g., fish
size, season)
Summer.
Average total
length 64.2
mm
SOURCE
Johnson and
Kucera (1985)
NOTES
Observations were made on the
habitat utilization of 801 age 0+
steelhead in three Clearwater
River tributaries, Idaho. Also
examined available habitat.
Bedrock Creek
18.8 cm ∀
8.1 (7.3 in
∀ 3.2)
Big Canyon Creek
17.8 cm ∀
12.9 (6.9
in ∀ 5.0)
Cottonwood Creek
16.8 cm ∀
12.5 (6.6
in ∀ 4.9)
Autumn.
Average total
length 84.5
mm
Johnson and
Kucera (1985)
Methods; see above
Bedrock Creek
17.0 cm ∀
10.1 (6.6
in ∀ 3.9)
Big Canyon Creek
18.8 cm ∀
12.6 (7.3
in ∀ 4.9)
Cottonwood Creek
0.30Β0.50
ft
(9.15Β15.2
4 cm)
June
sampling;
total length
ranged 32Β46
mm
(1.28Β1.84
in); average
total length =
36.5 mm
(1.46 in)
Sheppard and
Johnson (1985)
coho present. Range in which fish
Αpredominantly occurred.≅ N=20.
Summer flows were approximately
15Β20 cfs (0.42!0.57 ft 3 /s). ΑThe
utilization of areas with higher
current velocities in June may
reflect the actual physical
characteristics of the streams
rather than behavioral preferences
of these species because stream
discharge, and hence, mean
current velocities were higher
during the June sampling period.≅
0.60Β1.20
ft
(18.29Β36.
59 cm)
October
sampling;
total length
ranged 51Β86
mm
(2.04Β3.44
in); average
total length =
67.1 mm
(2.68 in)
Sheppard and
Johnson (1985)
steelhead present. Range in which
fish Αpredominantly occurred.≅
Flows in October were 60Β70%
lower than in June. N=42.
Stillwater Sciences
B-19
Appendix B
Table B-9. Age 0+ summer rearing (late summer/fall) for steelhead not related to depth or
velocity.
OTHER HABITAT CRITERIA
(e.g., substrate, cover type,
distance to cover, gradient,
minimum habitat area)
LIFE STAGE
NOTES
(e.g., fish size,
season)
SOURCE
NOTES
(e.g., methods, presence of other species,
complicating factors)
5.7 ∀ 0.43
Summer. Average
total length 64.2
mm
Johnson and
Kucera (1985)
Modified Wentworth scale: sand (4.0) gravel (5.0)
cobble (6.0) boulder (7.0) bedrock (8.0).
Bedrock Creek
5.9 ∀ 0.42
Big Canyon Creek
5.6 ∀ 0.42
Cottonwood Creek
6.2 ∀ 0.47
Autumn. Average
total length 84.5
mm
Johnson and
Kucera (1985)
Modified Wentworth scale: see above.
Bedrock Creek
6.1 ∀ 0.46
Big Canyon Creek
6.1 ∀ 0.40
Cottonwood Creek
Table B-10. Age 0+ winter rearing velocity criteria for steelhead.
VELOCITY CRITERIA
minimum
maximum
average
preferred/
optimal
0Β15 cm/s
(0Β0.49
ft/s)
LIFE STAGE
NOTES
(e.g., fish
size, season)
Size not
stated.
SOURCE
Bustard and
Narver (1975)
NOTES
87.1% of observations within this
range. Information collected by
snorkeling and electrofishing.
Velocities taken at focal points.
Focal point velocities for age 0+
and 1+ steelhead increased
significantly with rising
temperatures above 4 o C.
Temperatures during sampling
were generally less than 10 o C.
Table B-11. Age 0+ winter rearing depth criteria for steelhead.
DEPTH CRITERIA
minimum
maximum
average
preferred/
optimal
0Β15 cm
(0Β5.85 in)
LIFE STAGE
NOTES
(e.g., fish size,
season)
Size not stated.
SOURCE
Bustard and
Narver (1975)
NOTES
Age 0+ steelhead were strongly
associated with shallow water,
often less than 15 cm deep.
Information collected by
snorkeling and electrofishing.
Stillwater Sciences
B-20
Appendix B
Table B-12. Age 0+ winter rearing habitat criteria for steelhead not related to depth or
velocity.
LIFE STAGE
NOTES
(e.g., fish size,
season)
SOURCE
NOTES
Cover = rubble 10Β25 cm
(3.9Β9.75 in) diameter (>50%
observed under rocks <15 cm
(<5.85) diameter)
Bustard and Narver
(1975)
Information collected by snorkeling and
electrofishing. Age 0 and 1+ coho salmon present.
Pool or Channel Type = shallow
areas of low velocity near stream
margin
Bustard and Narver
(1975)
as above
Table B-13. Age 1+ and older summer rearing velocity criteria for steelhead.
VELOCITY CRITERIA
minimum
maximum
average
LIFE STAGE
NOTES
(e.g., fish size,
season)
SOURCE
12.8 cm/s
∀12.0
(0.42 ft/s
∀0.39
Estimated
mean
length=124 mm
(4.96 in) n=122
Shirvell (1990)
60Β90
cm/s
(1.97Β2.95
ft/s)
Age 1+,
Summer. FL >
100 mm
Everest and
Chapman
(1972)
19.4 cm/s
(0.64 ft/s)
ΑJuvenile≅
Moyle and Baltz
(1985) as cited
in Spence et al.
(1996)
Approx.
range
17Β32
cm/s
(0.56Β1.05
ft/s)
Total length
10.0 cm (3.90
in) September
to December
Smith and Li
(1983)
preferred/
optimal
NOTES
Mean of six samples during
altered flows using reservoir
releases; artificially placed
rootwads.
characteristics. Values given are
an average of values collected in
sympatric and allopatric
populations with chinook.
Ranges given are for focal point
velocities.
Focal point velocities measured at
locations where fish were
observed using direct observation
in Vas Creek, California. Fish
were then electrofished to obtain
length data. Relative habitat
availability was also determined.
Α...steelhead selected focal points
where water velocities were
higher than those typically
available in Vas Creek...our
results probably underestimate
mean water velocities at focal
points...≅ Invertebrate drift
increased with water velocity.
Data in this form is approximated
from Figure 2 on page 176 of
Smith and Li (1983).
Stillwater Sciences
B-21
Appendix B
VELOCITY CRITERIA
minimum
maximum
average
preferred/
optimal
Approx.
range
15Β35
cm/s
(0.49Β1.15
ft/s)
0.15 ft/s
(4.57 cm/s)
1.2 ft/s
(36.59
cm/s)
0.52 ft/s
(15.85
cm/s)
LIFE STAGE
NOTES
(e.g., fish size,
season)
SOURCE
NOTES
Total length
12.5 cm (4.88
in) September
to December
Smith and Li
(1983)
Methods, see above. Data on
larger fish is not included here
because the authors considered
their observations on larger fish
to be likely biased.
Mean total
length between
114 and 151
mm (4.56Β6.04
in)
Stuehrenberg
(1975)
characteristics.
Table B-14. Age 1+ and older summer rearing depth criteria for steelhead.
DEPTH CRITERIA
minimum
0.5 ft
(15.24 cm)
maximum
average
LIFE STAGE
NOTES
(e.g., fish size,
season)
SOURCE
56.5 cm
∀13.4
(22.04 in
∀5.23)
Estimated
mean
length=124 mm
(4.96 in) n=
122
Shirvell (1990)
60Β90 cm
(
1.97Β2.95
ft)
Age 1+,
Summer. FL >
100 mm (3.9
in)
Everest and
Chapman (1972)
63 cm
(24.57 in)
ΑJuvenile≅
Moyle and Baltz
(1985) as cited
in Spence et al.
(1996)
Mean total
length between
114 and 151
mm (4.56Β6.04
in)
Stuehrenberg
(1975)
preferred/
optimal
NOTES
(e.g., methods, presence of
other species, complicating
factors)
Mean of six samples during
altered flows using reservoir
releases; artificially placed
rootwads.
characteristics. Values given are
an average of values collected in
sympatric and allopatric
populations with chinook.
Ranges given are for focal point
velocities.
characteristics.
Stillwater Sciences
B-22
Appendix B
Table B-15. Age 1+ and older summer rearing for steelhead not related to depth or velocity.
LIFE STAGE
NOTES
(e.g., fish size,
season)
SOURCE
NOTES
Large substrate, >20 cm (7.80 in)
diameter.
Age 1+, Summer.
FL > 100 mm (3.9
in)
Everest and
Chapman (1972)
Highest densities of juvenile fish observed in a
range of habitat characteristics. Values given are
an average of values collected in sympatric and
allopatric populations with chinook. Ranges
given are for focal point velocities.
Table B-16. Age 1+ and older winter rearing velocity criteria for steelhead.
VELOCITY CRITERIA
minimum
maximum
average
preferred/
optimal
0Β15 cm/s
(0Β0.60
ft/s)
LIFE STAGE
NOTES
(e.g., fish size,
season)
SOURCE
NOTES
Age 1+
Bustard and
Narver (1975)
78 % of fish were associated with
water velocities <15 cm/s at
temperatures < 7 o C. Information
collected by snorkeling and
electrofishing. Velocities taken at
focal points. Focal point velocities
for age 0+ and 1+ steelhead
increased significantly with rising
temperatures above 4 o C.
Table B-17. Age 1+ and older winter rearing depth criteria for steelhead.
DEPTH CRITERIA
minimum
maximum
average
preferred/
optimal
Mainly >
45 cm
(17.55 in)
LIFE STAGE
NOTES
(e.g., fish size,
season)
SOURCE
NOTES
species, complicating factors))
Age 1+
Bustard and
Narver (1975)
Information collected by
snorkeling and electrofishing. Age
1+ steelhead occupied a wide
range of depths, but favored
depths significantly deeper than
age 0+ coho, and were found in
depths mainly greater than 45 cm.
Stillwater Sciences
B-23
Appendix B
Table B-18. Age 1+ and older rearing velocity criteria for steelhead [SEASON NOT SPECIFIED].
VELOCITY CRITERIA
minimum
maximum
LIFE STAGE
NOTES
(e.g., fish size,
season)
SOURCE
10 cm/s
(0.33 ft/s)
Age 1+
Hanson (1977)
as cited in
Spence et al.
(1996)
Race not specified.
15 cm/s
(0.49 ft/s)
Age 2+
Hanson (1977)
as cited in
Spence et al.
(1996)
Race not specified.
Age 3+
Hanson (1977)
as cited in
Spence et al.
(1996)
Race not specified.
Αjuvenile≅
Moyle and
Baltz (1985) as
cited in Spence
et al. (1996)
average
preferred/
optimal
15 cm/s
(0.49 ft/s)
19.4 cm/s
(0.64 ft/s)
NOTES
Table B-19. Age 1+ and older rearing depth criteria for steelhead [SEASON NOT
SPECIFIED].
DEPTH CRITERIA
minimum
maximum
LIFE STAGE
NOTES
(e.g., fish size,
season)
SOURCE
51 cm
(19.89 in)
Age 1+
Hanson (1977)
as cited in
Spence et al.
(1996)
Race not specified.
58 cm
(22.62 in)
Age 2+
Hanson (1977)
as cited in
Spence et al.
(1996)
Race not specified.
60 cm
(23.4 in)
Age 3+
Hanson (1977)
as cited in
Spence et al.
(1996)
Race not specified.
Stuehrenberg
(1975) as cited
in Spence et al.
(1996)
Race not specified
average
preferred/
optimal
18Β67 cm
(7.02Β26.1
3 in)
NOTES
Stillwater Sciences
B-24
Appendix B
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Appendix B
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Stillwater Sciences
B-32

Upper Penitencia Creek Limiting Factors Analysis Final Technical

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