Scott River Spawning Gravel Evaluation and Enhancement Plan

Transcription

Scott River Spawning Gravel Evaluation and Enhancement Plan
Scott River Spawning Gravel
Evaluation and Enhancement Plan
Submitted to:
Pacific States Marine Fisheries Commission
205 S.E. Spokane Street, Suite 100
Portland, OR 97202
&
California Department of Fish and Game
1455 Sandy Prairie Court
Fortuna, CA 95540
Submitted by:
Cramer Fish Sciences
13300 New Airport Road, Suite 102
Auburn CA 95602
In Partnership with:
Philip Williams & Associates, Ltd.
550 Kearny Street, Suite 900
San Francisco, CA 94108
&
The Siskiyou Resource Conservation District (SQRCD)
450 Main Street
Etna, CA 96027
i
EXECUTIVE SUMMARY
The Scott River Spawning Gravel Enhancement Plan (Plan) was developed through a
cooperative effort from Cramer Fish Sciences, The Siskiyou Resource Conservation District,
Philip Williams & Associates, California Department of Fish and Game, and the Pacific States
Marine Fisheries Commission. The document provides a description of the scientific approach
used to identify salmonid spawning habitat conditions and prioritize potential enhancement
locations and the results of the application of this approach on the Scott River Watershed. The
broad-level study approach has been designed to use best available data and field sampling to
assess watershed processes and determine potential impacts to salmonid spawning and
incubation habitat. The Plan provides watershed stakeholders with a framework for identifying,
quantifying and qualifying spawning habitat for anadromous salmonids within the Scott River
Basin and for prioritizing and strategizing the protection and maintenance of quality habitat as
well as enhancement of sub-optimal habitat. The Plan is programmatic in nature and accomplishes
the following:


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
Identifies the range of general salmonid spawning habitat conditions (i.e., substrate
quantity/quality, morphologic features) that exists in key reaches of the watershed.
Provides information on the most effective methods of spawning gravel enhancement currently
used.
Provides a basic monitoring and prioritization plan for the quantity and quality of salmonid
spawning habitat (emphasizing coho salmon) within the watershed. Note: the Plan can be used
not only to prioritize areas with the greatest potential for gravel enhancement but also for
identifying areas with greatest habitat quantity and quality presently.
Provides a simple tool for measuring potential, relative change in embryo survival from
enhancement actions within the watershed.
The ultimate goal of the Plan is to provide management tools that support the coexistence of a
productive, viable basin fishery, a healthy economy, and a valued quality of life for the
community of the Scott River Basin. The Plan is envisioned as a living document that will
continue to be refined as river rehabilitation moves forward, more scientific information on Scott
River salmonids is gathered, and more stakeholder outreach activities have been accomplished.
This Plan focuses on enhancing the quantity and quality of spawning gravels through
augmentation of sediment and structural habitat elements. It should be stressed that these are
short-term fixes. Spawning gravel management should be incorporated into the larger
framework of a watershed management plan.
General Results
Between 24 August and 16 October 2009, 33 of 51 river sub-reaches were sampled. Sample sites
represent ~1.4% (211m) of the total length of watershed channel (317021 m). The Reaches sampled
(218375 m) represent ~ 69% of the total watershed.
A legacy of historic impacts still bares its mark on channel morphology and riparian plant communities
of the Scott River Watershed. These historic effects comingle with modern impacts, affecting present
day physical habitat quantity and quality, and in turn, the ecology of the watershed.
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While there may be site specific caveats at a scale beyond this study (e.g. immediately below Etna
Reservoir; historically dynamited locations), observations suggest that the amount of coarse sediment
and its rate of delivery are not limiting overall spawning habitat availability in the Scott River
Watershed. However, elevated levels of fine sediment from natural and anthropogenic sources may
mask the presence and suitability of coarse sediment.
Monitoring identified existing levels of fine sediment that indicate impaired salmonid spawning areas.
Embryo survival modeling demonstrated a wide range of habitat quality, including very high and
extremely low survival estimates.
Occurrence of Large Woody Material (e.g. logs, rootwads, snags) in sampled streams is much less than
what the scientific literature suggests is needed for salmonids.
While there is extensive quality habitat for coho spawning there are also numerous areas where
improvements can be made. Specifically, there is an overall lack of LWM and an over-abundance of
confined channels in the lower watershed.
Ten (10) reaches within the Scott River watershed were identified as meeting the general requirements
for coho spawning habitat but demonstrating physical properties that were less than optimal for
spawning and incubation and having potential to benefit from gravel augmentation, structural
enhancement or a combination of the two. Recommended actions and potential enhancement tools are
identified for these reaches.
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TABLE OF CONTENTS
LIST OF FIGURES ..................................................................................................................................VI
LIST OF TABLES .................................................................................................................................VIII
PROJECT NARRATIVE........................................................................................................................... 1
Background ..................................................................................................................................1
LOCATION................................................................................................................................................. 3
Watershed Impacts.......................................................................................................................5
Historical..................................................................................................................................7
Modern 8
PROJECT PURPOSE ................................................................................................................................ 9
Overview......................................................................................................................................9
Priority Questions ........................................................................................................................9
Target Objectives .......................................................................................................................10
APPROACH.............................................................................................................................................. 12
Assessing Potential Spawning Habitat Availability Basin-wide ...............................................12
Compile, Analyze, and Summarize Existing Data.................................................................12
Study Delineation – Watershed Provinces........................................................................ 12
Review of Hydrologic Data Sources................................................................................. 14
Results from Hydrologic Data Sources............................................................................. 14
Spawning Habitat Assessment ...............................................................................................15
Study Reaches................................................................................................................... 15
Reach Connectivity........................................................................................................... 17
Habitat Quality.................................................................................................................. 20
Pool-Riffle Spawning Ground Sustainability ................................................................... 23
Results from Assessment of Pool-Riffle Spawning Ground Sustainability...................... 23
Quantifying Substrate Quality .......................................................................................... 23
Quantify Gravel Mobility Rates........................................................................................ 32
Estimation of Peak Runoff................................................................................................ 32
Results of Estimation of Peak Runoff............................................................................... 33
Sampling of Woody Material............................................................................................ 42
Results from Woody Material Sampling .......................................................................... 42
Identify Quantity and Quality of Potential Spawning Habitat Watershed Wide ...................44
Habitat Model Description and Output............................................................................. 44
Classification of Impacted Habitat and Potential Enhancement ............................................53
Recommended Actions ..........................................................................................................53
Model Results ........................................................................................................................53
SPAWNING GRAVEL ENHANCEMENT PLAN AND RECOMMENDED ACTIONS ................. 57
Potential Enhancement Tools ................................................................................................57
Gravel Injection ................................................................................................................ 59
Spawning Bed Enhancement ............................................................................................ 59
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Hydraulic Structure Placement ......................................................................................... 60
The Spawning Habitat Integrated Rehabilitation Approach ............................................. 63
Additional Considerations for Prioritization of Enhancement Projects.................................65
Estimating Costs ............................................................................................................... 66
Gravel Sources for the Scott River ................................................................................... 68
Reclamation ...................................................................................................................... 69
Permits and Approvals for Spawning Habitat Enhancement............................................ 69
CONCLUSIONS AND MANAGEMENT IMPLICATIONS...................................................73
Answers to Priority Study Questions .....................................................................................73
Use of the Scott River Spawning Habitat Management Plan ................................................75
Priorities for Spawning Gravel Management ................................................................... 75
Adaptive Management ...............................................................................................................78
Outreach.....................................................................................................................................79
ACKNOWLEDGEMENTS ..................................................................................................................... 79
LITERATURE CITED ............................................................................................................................ 80
APPENDIX A.
FLOW ANALYSIS ...................................................................................................I
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LIST OF FIGURES
Figure 1. Map of the Scott River valley with gauging stations and approximate locations of
study reaches. ................................................................................................................... 4
Figure 2. Historic spawning reaches for coho salmon in the Scott River watershed...................... 5
Figure 3. Historic wildfires of the Scott River Watershed. Courtesy of SQRCD. ......................... 7
Figure 4. Air photograph comparison near Fort Jones in A) 1944 and B) in 2010 and near
Etna in C) 1944 and D) 2010............................................................................................ 8
Figure 5. Study provinces of the Scott River watershed with annual precipitation..................... 13
Figure 6. Identification of sample reaches and reach breaks for the Scott River salmonid
spawning habitat study, July 2009 through July 2010. .................................................. 16
Figure 7. Percent gradient for Chinook salmon (left) and coho salmon (right). See Table 13
(below)............................................................................................................................ 17
Figure 8. Analysis of connectivity of streams in the Scott River watershed compared to
spawning period for coho and Chinook salmon. ............................................................ 18
Figure 9. Stream opening priority in the Scott River watershed................................................... 19
Figure 10. Detected natural and man-made barriers to adult salmonid passage in Scott
River Watershed. ............................................................................................................ 20
Figure 11. Identification of sampled and unsampled waters of the Scott River, July 2009
through July 2010. .......................................................................................................... 21
Figure 12. Relationship between channel morphology and reach averaged gradient
sampled in the Scott River Watershed, California. Squares = mean; Whiskers =
min and max. .................................................................................................................. 23
Figure 13. Sustainability of riffle pool units studied. ................................................................... 24
Figure 14. Proportional distribution of female coho salmon fork length (mm FL) in the
Scott River watershed. All data collected between 16 November 2004 and 17
January 2005................................................................................................................... 27
Figure 15. Gravel composition (D50) in the Scott River watershed; data provided by pebble
count surveys .................................................................................................................. 28
Figure 16. The relationship between substrate size classes (0.85 and 9.5 mm) and salmon
embryo survival. Data taken from Tappel and Bjornn (1983) to build regression
models). .......................................................................................................................... 29
Figure 17. Results of embryo survival model with survival to emergence in the Scott River
watershed. ....................................................................................................................... 31
Figure 18. Normalized average bedload transport among study reaches of the Scott River
Watershed, California..................................................................................................... 34
Figure 19. Estimated transport rate for coho-appropriate spawning gravel sizes per study
reach. .............................................................................................................................. 35
Figure 20. Sediment Supply Index for study reaches of Scott River Watershed, California. ..... 36
Figure 21. An example of the Scour chains used to determine sediment mobility. ..................... 38
Figure 22. Estimated timing of Chinook and coho salmon spawning and incubation for the
Scott River, CA. ............................................................................................................. 39
Figure 23. Length frequency of female coho salmon observed during carcass surveys of the
Scott River, California. Data from SQRCD surveys. ..................................................... 40
Figure 24. Estimated redd depths for coho salmon length frequencies for Scott River,
California. ....................................................................................................................... 41
Figure 25. Density (percent surface area coverage) of woody material (>3 in diameter)
within study reaches of the Scott River.......................................................................... 43
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Figure 26. Prioritization of coho salmon spawning habitat. ......................................................... 44
Figure 27. Median diameter (D50) of spawning gravel plotted against body length of a
spawning salmonid. Solid squares denote samples from redds; open triangles are
‘‘unspawned gravels,’’ which are potential spawning gravels sampled from the
undisturbed bed near redds (in Kondolf 2000 as modified from Kondolf and
Wolman 1993). ............................................................................................................... 47
Figure 28. Predicted potential spawning reaches using substrate size and estimated reach
gradient. Coho salmon redds identified during three years of surveys are overlaid.
Black indicates no physical data collected. .................................................................... 48
Figure 29. Classification process of enhancement potential......................................................... 50
Figure 30. Percent fines in the Scott River watershed. ................................................................. 51
Figure 31. Regression model for coho spawning density as it relates to pool spacing
(Montgomery et al. 1999)............................................................................................... 52
Figure 32. Pool ratio in the Scott River watershed (Channel width/pool).................................... 52
Figure 33. Gravel injection below Englebright Dam, Yuba River, California. Photo
courtesy of U.S. Army Corp of Engineers. .................................................................... 59
Figure 34. Strategic gravel placement on the lower American River, California......................... 60
Figure 35. Fall-run Chinook salmon spawning adjacent to large boulders placed in lower
Mokelumne River, CA. Log jam placed adjacent to spawning gravel to provide
heterogeneity. ................................................................................................................. 63
Figure 36. Conceptual spawning habitat model. The arrows indicate influences, the circles
represent processes and characteristics, and the boxes are the results. .......................... 64
Figure 37. The SHIRA flowchart. The two primary components are phases and modes.
Projects progress sequentially through specific project phases, ranging from the
initial problem identification to long-term monitoring and adaptive management.
During each of seven phases, four primary modes are used to collect and analyze
data on which informed decisions can be based (from Wheaton et al. 2004). ............... 65
Figure 38. Potential gravel sources near the Scott River; Dredger tailings. ................................. 69
Figure 40. Basic flow diagram of adaptive management activities. ............................................. 78
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LIST OF TABLES
Table 1. Historical disturbance within the Scott River Watershed. ................................................ 6
Table 2. Physiographic regions of the Scott River watershed and associated parameters. .......... 13
Table 3. Summary of streamflow records in the Scott River watershed. ..................................... 14
Table 4. Reported ranges of slope and channel morphology........................................................ 15
Table 5. Results of pebble counts and core samples within the Scott River Watershed. ............ 25
Table 6. Recommended gravel mixture for Scott River coho salmon spawning.......................... 27
Table 7. The estimated relative survival of salmon embryos in relationship to fine sediment
in the Scott River watershed, California......................................................................... 30
Table 8. Calculated peak runoff for study reaches within the Scott River Watershed,
California. ....................................................................................................................... 33
Table 9. Estimated redd depths for coho salmon length frequencies observed in the Scott
River, California. ............................................................................................................ 40
Table 10. Information on scour chain stations installed throughout the Scott River
Watershed October 2009 and recovered July 2010 ........................................................ 41
Table 11. Estimation of LWM from sampled reaches of the Scott River watershed. .................. 42
Table 12. Relative priority of channel gradient for spawning by Chinook and coho salmon
(Montgomery et al. 1999)............................................................................................... 46
Table 13. Relative use of four primary stream habitats by Chinook and coho salmon
(Buffington et al. 1999). ................................................................................................. 46
Table 14. Study reaches that met initial screening criteria in Chart 1. ......................................... 49
Table 15. Classification of impacted habitat and potential rehabilitation action.......................... 53
Table 16. A summary of salmonid spawning habitat enhancement/ augmentation
techniques. ...................................................................................................................... 58
Table 17. Primary functions of instream structures in habitat applications. Source: Taken
from Washington Department of Fish and Wildlife (2004). .......................................... 62
Table 18. Stewardship prioritization in the Scott River watershed. ............................................. 67
Table 19. Approximate cost (2010 year dollars) for common varieties of timber in Siskiyou
County. Assume USD $0.06 – $0.10 km-1 for transportation costs from harvest
location to enhancement site per log. Logs containing rootwads and/or canopy
will be much more expensive. ........................................................................................ 68
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PROJECT NARRATIVE
Background
The Scott River watershed supports populations of coho salmon Oncorhynchus kisutch, Chinook
salmon O. tshawytscha, and steelhead O. mykiss and may hold the largest abundance of native
coho salmon in the Klamath River basin tributary systems (Brown et al. 1994). The Scott River
is important habitat for these populations and has been designated as a Scenic and Recreational
River within the National Wild and Scenic Rivers System. The designation extends from the
river’s confluence with the Klamath to its confluence with Schackleford Creek. A range of
anthropogenic factors has contributed to the decline of Scott River salmonid populations.
Decades of gravel and gold mining, stream channelization, and extensive beaver harvest have
impacted the quality and quantity of available habitat for spawning and rearing. Spawning
gravels have been depleted, stream systems have been simplified, and high quality rearing
habitat has been dramatically reduced. When these impacts are combined with intensive
agriculture, the geology and low gradient morphology of the area, and a warming, drying
climate, the productivity of the habitat for salmon and steelhead has been degraded and reduced.
The Scott River watershed has been listed as impaired in relation to sediment since 1992, and
impaired in relation to temperature since 1998, pursuant to Section 303(d) of the Clean Water
Act.
Spawning surveys are conducted each year by California Department of Fish and Game (CDFG),
Siskiyou Resource Conservation District (SQRCD), and the U.S. Forest Service (USFS) for fallrun Chinook salmon; information for coho salmon and steelhead is more limited. Some
information on coho salmon has been provided by Maurer (2002) who provided information on
distribution and run timing, sampling for genetic testing, and flow summaries, as well as
recommendations for continued surveys with abundance estimates; and, Quigley (2005) who
completed limited coho spawning surveys. Less than 600 fall-run Chinook salmon returned in
1992, although fluctuations occurred from 1991 –1996 when escapement estimates ranged from
586 – 13,511. In recent years, as few as an estimated 789 fall-run Chinook salmon returned to
the basin (CDFG 2007). Coho salmon have exhibited similar declines, and are currently listed as
Threatened by the Federal and California Endangered Species Act (CESA).
Major impacts leading to the decline of spawning habitat in the Scott River have included nonpoint source water quality impairments such as excessive sediment and temperature levels
(NCRWQCB 1995; Black 1998), impacts from historical mining operations (Watershed Sciences
2004), land-use practices and water development (West et al. 1989; Moyle et al. 2003). Several
mitigation measures, including flow augmentation, fine sediment storage facilities, riparian
vegetation replanting, road management, gravel cleansing, placement of large woody material
(LWM) structures, construction of spawning channels, and screening of active water diversions
have been suggested with varying degrees of implementation (West 1984; DWR 1991; Mount et
al. 2003; Quigley 2003). The Shasta-Scott Coho Recovery Team (SSRT) made
recommendations summarized in seven categories: Water Management, Water Augmentation,
Habitat Management, Water Use Efficiency, Protection, Assessment and Monitoring, and
Education and Outreach (SSRT 2003). Throughout the Scott River watershed, many individuals,
groups, and agencies have been working to enhance and restore fish habitat and water quality.
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These groups include, but are not limited to: the SQRCD; the Scott River Watershed Council; the
French Creek Watershed Advisory Group; private timber companies; Siskiyou County and the
Five Counties Salmon Conservation Process; the CDFG; the California Department of Water
Resources; the USFS; the Scott River Water Trust and, the Klamath River Basin Fisheries Task
Force. Preliminary work on the quality and quantity of spawning habitat has been implemented
over the past 20 years (Sommarstrom et al. 1990; Quigley 2008), but a thorough evaluation and
documentation has not been completed. The preliminary assessment of gravel quality along the
Scott River and associated tributaries provides the foundation for a more in-depth assessment
(Sommarstrom 2001; Quigley 2008). The SSRT recommended continuing and expanding
existing surveys, quantifying spawning habitat, and using this information to prioritize projects
for habitat restoration and enhancement (SSRT 2003). In the initial phase of the Scott River
Watershed Council Strategic Action Plan (2006), it was recommended that a detailed assessment
of factors limiting spawning, migration, and rearing affecting stream systems should be
completed. This includes a study to determine the effects of dredger tailings on the Scott River
floodplain and a stream habitat condition inventory of the watershed to determine what
treatments may be needed and might be effective in improving upper valley stream function.
The Recovery Strategy for California coho salmon (CDFG 2004) also identifies a watershed
sediment budget and a detailed assessment of spawning gravels in the Scott River basin as a high
priority to develop an effective, long-range management plan. Additionally, the 2008 Scott
River Watershed-wide Permitting Program Incidental Take Permit (ITP) requires the
development of a Spawning Gravel Enhancement Plan to guide the enhancement of spawning
grounds for coho salmon as part of the mitigation program for the impacts caused by activities
authorized by the Permitting Program. Expanding and completing work initiated in these
studies, including developing a list of prioritized gravel augmentation sites, if warranted, will
build a strong foundation for future spawning ground restoration and enhancement.
The following Scott River Spawning Gravel Enhancement Plan (Plan) has been developed
through the cooperative effort of Cramer Fish Sciences (CFS), SQRCD, Philip Williams &
Associates (PWA), CDFG, and the Pacific States Marine Fisheries Commission. The following
document provides a detailed description of the scientific approach used to identify habitat
conditions and prioritize potential locations for enhancement, and the results of the application of
this approach on the Scott River watershed as well as a description of techniques that can be used
in rehabilitation. The study approach has been designed to use the best available data and field
sampling to assess watershed processes and determine potential impacts to salmonids. This is a
broad-level approach, providing generalized information best used for prioritization and planning
of restoration projects. The area sampled is only a fraction (< 5%) of the watershed, and we
understand how various habitat processes (e.g., large woody material or boulder deposition,
encroachment by vegetation), occurring at smaller than reach-level scales, may have been missed
in this assessment. It is important to conduct further monitoring after sites for enhancement have
been identified, so habitat processes can be understood with greater confidence prior to
restoration actions.
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LOCATION
The Scott River Basin is located in south-central Siskiyou County, California, about 30 miles
south of the Oregon border (Figure 1). The Scott River is a principal tributary of the Klamath
River and has an annual discharge of 489,800 acre-feet (U.S. Geological Survey (USGS) gage
station). The basin is 813 square miles (2,106 km2) in area with elevation ranging from 8,300 ft
(2,530 m) in the Marble and Salmon mountains to just under 2,000 ft (610 m) at the river’s
mouth (SWRCB 2007). The Scott River originates in snow-fed headwaters on primarily U.S.
Forest Service lands, slows down (River Mile (RM) 56) in the large alluvial Scott Valley (about
70,000 ac [28,328 ha]) composed of private farmland, and then drops (RM 21) again into a
narrow forested canyon of mostly public land. Rainfall at Fort Jones in Scott Valley averages
17.47 in (44 cm) (Sommarstrom 2001). The river basin is a narrow alluvial floodplain that is
about 28 mi (45 km) long and up to 4 mi (6.4 km) wide. The basin is located within the eastern
portion of the Klamath Mountains and consists of bedrock from metasedimentary and
metavolcanic rocks of Late Jurassic and possibly Early Cretaceous Age. The alluvial fill in the
valley contains unconsolidated Pleistocene and recent deposits with an extensive area of
granodioritic rock, a light-colored, coarse material that is noncohesive and high erodible (Laake
1979; Sommarstrom et al. 1990). The basin is bounded to the north and northwest by the Scott
Bar Mountains, and by the Salmon Mountains to the west and southwest. The Scott Mountains
bound the south and southeast part of the basin, and to the east are the Trinity Mountains.
Annual precipitation within the basin is estimated to be 21 – 25 in (53 – 64 cm). Historic and
current spawning areas are shown in Figure 2.
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Figure 1. Map of the Scott River valley with gauging stations and approximate locations of study reaches.
4
Figure 2. Historic spawning reaches for coho salmon in the Scott River watershed.
Watershed Impacts
The modern Scott River Watershed has a legacy of natural and anthropogenic disturbances. Large scale natural
disturbances in the watershed include fire and flooding both of which can result in excessive amounts of water,
wood, and sediment being delivered to downstream reaches (
Table 1). Recent significant fire events include the 1955 Kidder Creek Fire and the 1987 fires in
the head waters of Thompkins and Kelsey creeks (Figure 3). Recent significant flood events
include the 1964, 1995, and 1997 winter storms. Historic and modern anthropogenic impacts in
the watershed include mining, road building, dams, diversions, cattle ranching, agriculture,
logging, beaver eradication, stream straightening and confinement by levees, bank stabilization,
and water withdrawals.
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Table 1. Historical disturbance within the Scott River Watershed.
Watershed
Disturbance
Crater Creek
Road building, mining and logging. Unknown fire history. Potentially suffered debris torrent in 1997 flood.
Grouse Creek
Road building, mining and logging.
South Fork Scott River
French Creek
Etna Creek
Patterson Creek
Kidder Creek
Shackleford Creek
Extensive historic placer mining. Road building and logging since 1950s - 1960s. Unknown fire history
Granitic watershed. Mining. Road building and logging. Unknown fire history.
Unknown mining history. Road building and logging. Limited documented fire history. Lower alluvial
section redirected from historic alignment and straightened.
Unknown mining history. Road building and logging. Large fire in 1955 in middle of watershed. Lower
alluvial section straightened and potentially realigned.
Massive fire in 1955 followed by 1955 flood caused significant channel failure in alluvial area. Road
building and logging. Areas of alluvial section leveed and potentially straightend and realigned.
Significant historic mining. Road building and logging. Limited documented fire history. Areas of alluvial
section leveed, rip rapped and potentially straightened and realigned.
Moffet Creek
Areas of highly erodible geology. Significant road building and logging. Documented areas of mass wasting
along the channel. Several documented fires in watershed.
Canyon Creek
Unknown mining history. Road building and logging. Several documented fires in watershed.
Tompkins Creek
Scott River
Road building and logging in 1980s. Large amount of headwaters of watershed burned in 1987. Debris
torrent during 1997 flood.
Beaver removal and extensive placer mining during 19th century. Army Corps of Engineers straightened,
cleared and leveed a section from approx. Etna Creek to Fort Jones in 1938. Dredging north of Callahan
(1935 to ~1950) created tailing pile. Leveed and rip rapped areas from late 1950's to 1990's.
6
Figure 3. Historic wildfires of the Scott River Watershed. Courtesy of SQRCD.
Historical
In the 1830’s beaver eradication in the Scott Valley was widespread (Sommarstrom et al. 1990).
This potentially would have been devastating for resident coho salmon who frequently occupy
areas close to beaver dens for rearing. In the 1850’s gold was discovered in Scott Bar triggering
increased interest in the valley as a resource. In the next decade, large floods pushed the valley
to the East as widespread placer mining was beginning to take place. By the end of the century
the South Fork, Oro Fino, and Shackleford creeks as well as the mainstem Scott River were
being mined for Gold. In the early to mid 1900’s agricultural use of the lowland valley increased
with cattle and hay operations. Gold dredging began taking place in the 1930’s to 1940’s on the
upper reaches of the mainstem Scott River and in Wildcat Creek. Road building and logging
began to increase in the 1950’s as the watershed became a productive area for timber harvest.
Concurrently, much of the mainstem Scott River and its tributaries in the lowland valley became
straightened, leveed, and armored. Agricultural diversions of water began to increase from this
time to the present day. Like many California watersheds, the Scott River has a legacy of
extensive land use change and associated disturbance to the natural environment.
A comparison of aerial photographs from 1944 to the present readily demonstrates the extent of
land use change and river impacts in the lowland valley sections of the Scott River Watershed
(Figure 4). Anthropogenic impacts have resulted in a lack of channel complexity from channel
straightening and reduced amounts of woody material. As late as 1944 the mainstem Scott River
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was still a complex channel with single-thread meandering, anabranching1, and braided channel
morphologies. The present-day mainstem Scott River bares minor resemblance to its more
complex form of 1944 although meandering and straight channel planforms are still present. The
cumulative effect of these changes cannot be quantified, but it is clear that both the amount and
quality and physical habitat has been
reduced.
Figure 4. Air photograph comparison near Fort Jones in A) 1944 and B) in 2010 and near Etna in C) 1944
and D) 2010.
Modern
Modern impacts in the Scott River watershed include stream modification from agricultural
activities in the lowland valley, logging in the upper watersheds, and flow diversions throughout
the basin. While the legacy of historical impacts still affect stream conditions this gravel plan
will hopefully aid stakeholders in making scientifically based management decisions that best
utilize the resources of the Scott River watershed.
Mining and logging are two legacy impacts that are still affecting the potential of the Scott River
watershed to support viable salmonid populations. Past gravel mining excavation continues to
directly affect the size range of stream bottom gravels (and thus the quality of this physical
habitat). Channel confinement by historic mining tailings indirectly affects the diversity of
1
A type of distributary river channel that separates from its trunk stream and may flow parallel to it for several
kilometers before rejoining it.
8
stream habitat that might otherwise be available. Many of these tailing piles are too large for the
adjacent watercourse to reshape. This has the effect of creating hydraulic conditions similar to
bedrock canyons where sediment used by salmonids has a lower likelihood of persistence due to
increased (or more efficient) sediment transport compared to unconfined reaches. The overextraction of streambed alluvium may also have stripped the alluvial cover from some river
reaches exposing underlying bedrock – the net result of which is enhanced sediment transport,
less persistent alluvium, and an overall loss of physical complexity. A full historical analysis
would be needed to determine if and where this is the case.
Logging in the watershed was historically widespread. Direct effects of logging include the
removal of large streamside trees that would have created hydraulic diversity while persisting
through large flood events. Indirectly, logging reduces the amount of woody material supplied to
streams as well as the age and strength of logs available for recruitment to a stream. Woody
material must be of a certain size and strength to withstand hydraulic forces typical of flood
stages (Abbe and Montgomery 1996). When woody material recruited by the stream is of
inadequate age and size, the persistence of wood-related morphologic features is notably less
(Brown and Blomberg 2009). Cumulatively this results in less available physical habitat for
salmonids and reduced quality for existing habitat.
PROJECT PURPOSE
Overview
The Scott River Spawning Gravel Evaluation and Enhancement Plan (Plan) has been prepared
for the CDFG and Pacific States Marine Fisheries Commission, in collaboration with the
SQRCD. The Plan identifies areas where gravel for salmonid spawning (emphasizing coho
salmon), could be effectively placed to improve habitat conditions. The Plan considers how
gravels are recruited in the potential areas, and prioritizes gravel enhancement projects
throughout the entire watershed. This project evaluates the quantity, quality, distribution, and
sources of existing coarse sediment and spawning gravel supplies, and determines the
appropriateness of spawning gravel augmentation in the Scott River and tributaries in Siskiyou
County. Based on the results of this evaluation, we have developed this Plan which identifies
areas of high quality spawning habitat that should be protected and maintained, recommends
spawning gravel enhancement actions, identifies potential watershed reaches for spawning gravel
augmentation, specifies augmentation methods and volumes, develops sediment composition
specifications, and recommends initial augmentation sources. The Plan also identifies reaches
where spawning habitat structures could enhance and/or retain existing gravel supplies and
provides recommendations for priority stream reaches where spawning gravels should be
augmented.
Priority Questions
The development of the Gravel Enhancement Plan has been designed to address the following
priority questions:
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
Is spawning gravel available at strategic locations in the watershed that allow emergent
fry access to suitable rearing habitat?

Is the rate of coarse sediment delivered to spawning reaches in the Scott River (upper
river and canyon reach) and in its tributaries limiting spawning habitat availability of
current and projected population targets?

Is the quality of the existing spawning gravel impaired by excessive fine sediment?

Will survival of eggs to emergent fry be increased as a result of the project?
Specifically, we wanted to determine coarse sediment supply, assess habitat quality and quantity,
and perform statistical analyses of Scott River Watershed hydrology and geomorphology to
address these questions. The overall goals of this gravel evaluation and enhancement plan are to
provide a robust assessment of existing and historic conditions, provide habitat maps, hydrology
assessment, robust comparisons in gravel quality and quantity, and identify priority sites for
gravel augmentation, including recommendations for additions of instream structures.
Target Objectives
The overall goal of the proposed project is to evaluate the quantity, quality, distribution and
sources of coarse sediment supply in the Scott River watershed, in specified reaches (see Study
Delineation section). The project has the following target objectives:

Coordinate with CDFG and SQRCD on obtaining landowner permission; coordinate all
project activities with SQRCD and landowners.

Obtain aerial photos with sufficient resolution for habitat mapping and classify available
habitat; create a field sampling plan to ground-truth habitat analysis results.

Conduct field sampling and collect habitat information at randomly-selected, replicated
(by type) locations in each reach for ground-truthing; delineate habitat type with submeter Global Positioning System (GPS); create and populate a Geographic Information
System (GIS) database with information on gravel quality (see below).

Assess gravel quality in terms of size composition, and proportion of fine sediment;
process core samples at USGS-certified laboratory; combine data with location
information in spatial database.

Use scour core methods at randomly-selected spawning habitat locations to measure
hydraulic thresholds for surface particle mobility, bed scour depths, and sediment redeposition depths.

Compile and analyze existing stream flow data in the Scott River

Evaluate the need for spawning habitat structures to enhance and/or retain existing gravel
supplies and, if deemed necessary, recommend at least five priority stream reaches where
habitat structures would enhance ecosystem function.
10

Analyze field data to inform the gravel evaluation; develop recommendations and
priorities for gravel augmentation; identify priority sites for gravel augmentation.

Develop Scott River Spawning Gravel Evaluation and Enhancement Plan (Plan) to
describe project activities, methods, results, and recommendations; include a monitoring
plan, describing geomorphic monitoring (i.e., sediment mobility and transport processes),
spawning gravel quantity, quality, and distribution, frequency of mobilization, and
spawning gravel utilization by adult salmonids.
While the Plan provides technical information on existing conditions and on restoration and
enhancement methods, it is programmatic in nature and accomplishes the following:

Identifies the range of general salmonid spawning habitat conditions (i.e., substrate
quantity/quality, morphologic features) that exists in key reaches of the watershed.

Provides information on the most effective methods of spawning gravel enhancement
currently used.

Provides a basic monitoring and prioritization plan for the quantity and quality of
salmonid spawning habitat (emphasizing coho salmon) within the watershed. Note, the
Plan can be used to not only prioritize areas with the greatest potential for gravel
enhancement but also for identifying areas with greatest habitat quantity and quality
presently.

Provides a simple tool for measuring potential, relative change in embryo survival from
enhancement actions within the watershed.
It is important to note that similar to all lotic systems, the Scott River is dynamic and constantly
going through natural, including climatic, and anthropogenic changes that will alter much that
was observed in past and present (August 2009 and July 2010) monitoring data sets. This
dynamic nature demands continued monitoring and vetting of information. It is also important to
note that gravel augmentation and structural enhancement are just that, augmentation and
enhancement. Management and/or restoration of watersheds requires overall management of
watershed processes, including hydrology, sediment, water quality, vegetation, resource harvest,
land management, and the effects of linked watersheds etc. Addressing the entire list is beyond
the scope of this project. We hope the prioritization system developed here will facilitate the
ongoing process of watershed management, and will provide a framework for evaluation of, and
making recommendations on, the quality and management of salmonid spawning gravels within
the Scott River Watershed.
The following information provides descriptions and use for the evaluation process
recommended to identify and prioritize potential gravel augmentation and structural placement
enhancement sites in the Scott River Watershed.
11
APPROACH
Assessing Potential Spawning Habitat Availability Basin-wide
Habitat requirements for persistence of “focal species” define the attributes that must be present
if that landscape is to meet the requirements of the species that occur there. The needs of focal
species can be used to develop explicit guidelines regarding the composition, quantity, and
configuration of habitat patches and the management regimes that must be applied to the
resulting design (Lambeck 1997). For the purposes of identifying key physical parameters for
the Scott River, we chose coho salmon as the focal species because its spawning requirements
overlap with the two other anadromous salmonids in the watershed (Chinook salmon and
steelhead) and because the coho population is presently the most imperiled salmonid in the
watershed. The following provides the details and results of our approach. We have developed a
scientifically rigorous system, using pre-existing and field-collected data, to assess habitat
quantity and quality and prioritize habitat availability and rehabilitation potential within the Scott
River basin. This approach has resulted in the identification of “non-habitat”, high quality
habitat areas, and those sites with potential for improvement. “Non-habitat” by no-means
suggests the habitat is unimportant. It simply identifies areas that do not meet the basic
requirements for what we identify as coho salmon spawning habitat. In the following section,
we describe the existing data, how habitat types and reaches were delineated, factors included to
analyze habitat quality, potential enhancement tools, and the prioritization systems for reaches.
How this approach was applied to the Scott River Basin and the results of applying this approach
are described in the next section below (Results).
Compile, Analyze, and Summarize Existing Data
Study Delineation – Watershed Provinces
Study reaches were determined by hierarchically examining physiographic properties of the
Scott River Basin at different scales. For the watershed scale, we broke the watershed up into
study providences using climate and relief (a surrogate for geology) as first order filters of the
watershed, because they are dominant exogenous controls on stream morphology and resulting
physical habitat (Grant and Swanson 1995; Montgomery et al. 1995, 1996; Bisson et al. 2006).
Using the digital elevation model and mean annual precipitation isohyetal layers, we
qualitatively subdivided the Scott River watershed. Our initial screening at the watershed scale
resulted in six physiographic drainages: East, West-Dry, West-Wet, Canyon, Southwest, and
South (Figure 5; Table 2). We further noted the occurrence of decomposed granitic soils
(Sommarstrom 1990). At the reach scale, valley width and slope were used to subdivide streams
within the above study basins longitudinally because these two variables drive fluvial
geomorphic processes (Buffington et al. 2004; Bisson et al. 2006; White et al. 2010).
12
Figure 5. Study provinces of the Scott River watershed with annual precipitation.
Table 2. Physiographic regions of the Scott River watershed and associated parameters.
Morphology
Area (sq. mi.)
Canyon
121.0
West-Wet
179.4
West-Dry
54.7
East
282.0
South East
124.6
Southwest
52.0
*DG = decomposed granite
DG* (% Area)
NA
17%
59%
NA
8%
73%
Precipitation
Approximate Max.
Elevation (ft)
8300
8300
8000
6000
8550
7800
13
Max. Mean Annual
Precipitation (in)
85
65
55
35
33
47
Avg. Mean Annual
Precipitation (in)
54
44
37
28
26
33
Snow
Yes
Yes
Yes
No
Yes
Yes
Review of Hydrologic Data Sources
Streamflow is considered the master variable in fluvial systems and ultimately all decision
making rests on reliable hydrologic data for a sufficient period of time to obtain statistically
relevant results. Our team reviewed streamflow data sources within the Scott River watershed to
identify data gaps that may aid CDFG and the SQRCD in assessing stream behavior. Discharge
records have been primarily focused on the mainstem Scott River and date back to 1910 (Table
3). From those early times, the USGS has operated and maintained several gages in the basin,
but the operations of many have shifted responsibility to the California Department of Water
Resources. Moreover, the SQRCD has begun operating gages on tributary sites.
Table 3. Summary of streamflow records in the Scott River watershed.
Province
Site
Station ID
Operator
Type(s) of Data
East Fork Scott River at
Callahan
F26050
DWR
15-min, daily mean, daily min/max
2002-2003,
2005, 2007
EF Scott R NR Callahan
CA
11518000
USGS
Daily data, daily statistics, monthly
statistics, annual statistics
1910-1911
EF Scott R Callahan
11518050
USGS
Daily data, daily statistics, monthly
statistics, annual statistics, peak
streamflow
1960-1974
EF Scott R BL Houston
C NR Callahan CA
18010208
USGS
Daily data, daily statistics, monthly
statistics, annual statistics, peak
streamflow
1970-2006
EF Scott R AB Kangaroo
C NR Callahan CA
11517950
USGS
Daily data, daily statistics, monthly
statistics, annual statistics, peak
streamflow
1970-2006
South Fork Scott River
near Callahan
F28100
DWR
15-min, daily min, mean, and max,
rating table
2002-2003,
2005, 2007
SF Scott R NR Callahan
CA
11518200
USGS
Daily data, daily statistics, monthly
statistics, annual statistics, peak
streamflow
1958-1960
East/
Mainstem
Scott River near Scott
Bar
F25040
DWR
15-min, daily mean, daily min/max
2005-present
Canyon/
Mainstem
Scott River near Fort
Jones
11519500
USGS
Real-time, daily data, daily
statistics, monthly statistics, peak
streamflow
1941-present
Mill Creek near
Mugginsville
F25480
DWR
15-min, daily min/max
2005-present
Southeast
Southwest
West Side Wet
Shackleford Creek near
Mugginsville
West Side Dry
French Creek near HWY
3
Years
Available
2004-present
F25650
DWR
15-min, daily mean, daily min/max
2005-present
Results from Hydrologic Data Sources
There has been an increase in Scott River basin streamflow gages since the first gage was
installed in 1910. Moreover, the range of gages has also increased to tributaries of the mainstem
covering a greater geographic scope. However, streamflow estimates from the East province
appear to be lacking. Also, long term data that can be considered statistically significant for
hydrologic analysis is lacking in tributary gages. Our recommendations are that gages be
14
operated and maintained in the physiographic provinces outlined in this study. This will allow
stakeholders to objectively evaluate streamflow in lieu of geographic diversity in the Scott River
watershed.
Spawning Habitat Assessment
Study Reaches
The existing slope (i.e., gradient) GIS layer developed by the Institute for Forest and Watershed
Management – Humboldt State University Foundation (Lamphear 2004) was utilized to identify
breaks in slope. These gradient breaks and a qualitative assessment of changes in valley width
were used to delineate study reaches within the selected tributaries and main stem Scott River.
Streams were visually assessed for viable physical habitat using known relationships between
channel morphology and slope (Table 4; Figure 6; and Figure 7). Valley widths were
qualitatively delineated into canyon, transition, and valley segments (Grant and Swanson 1995;
Bisson et al. 2006). Within this framework, local knowledge of the watershed was used to
determine study sites based on landowner access, stream accessibility and presence and absence
of spawning from past monitoring.
Table 4. Reported ranges of slope and channel morphology.
Position
Slope Range*
Morphology
Valley
< 1%
Free Pool Riffle
Upper Valley/Canyon
1 – 2%
Forced Riffle Pool/Plane Bed
Canyon
2 – 5%
Plane Bed/Step Pool/Forced Pool
Headwaters
> 5%
Step-pool/Cascade/Bedrock Controlled
15
Figure 6. Identification of sample reaches and reach breaks for the Scott River salmonid spawning habitat
study, July 2009 through July 2010.
16
Figure 7. Percent gradient for Chinook salmon (left) and coho salmon (right). See Table 13 (below).
Reach Connectivity
Timing of Stream Opening
In order for streams to be considered for spawning habitat, they must be accessible at the
appropriate time for focal salmonids to use them. That is, the stream that holds the habitat must
connect to waterways further downstream at times when adults are migrating upstream, and
during the spawning season. We used weir counts redd and carcass survey reports from Maurer
(2002), SQRCD (2007) and CDFG weir counts, as reported in USFWS (1998), to identify adult
migration timing of coho and Chinook salmon. We then used the available flow data for our
primary stream reaches along with field surveys to identify when each of these reaches became
connected to the lower system (APPENDIX A.
FLOW ANALYSIS; Figure 8 and Figure 9).
17
Reach
Stream
Mainstem 1
Scott River (Canyon)
Mainstem 2
Scott River (Ft Jones)
Mainstem 3 Scott River (Below Youngs Dam)
Mainstem 4 Scott River (Above Youngs Dam)
Mainstem 5
Scott River (Tailings)
Study Drainages
Canyon
West side
Wet
West side
Dry
South West
South East
Spawning
Period
Species
East Side
Priority
Medium
High
?
?
Tompkins Creek
Canyon Creek
Shackleford Creek
Kidder Creek
Patterson Creek (Etna)
Patterson (Ft Jones)
Etna Creek
French Creek
Sugar Creek
South Fork Scott River
Wildcat Creek
Grouse Creek
Crater Creek
East Fork Scott River
Indian Creek
Moffett Creek
Rattlesnake
?
?
Low
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
?
1
2
3
4
1
2
3
4
Always Connect
Always Connect
1Disconnected until Mainstem opens
?
?
?
?
Always Connect
Coho
Time
Period
Chinook
Week
Month
1
2
3
4
1
2
October
3
November
4
December
Stream disconnected or non-spawning period
Range of period when stream has been know to connect
Consistently connected
Spawning period
Figure 8. Analysis of connectivity of streams in the Scott River watershed compared to spawning period for coho and Chinook salmon.
18
January
Figure 9. Stream opening priority in the Scott River watershed.
Physical Barriers
We used a combination of data from Calfish, a collaborative website that provides access to
anadromous fish datasets (e.g., anadromous abundance, barriers, and restoration projects;
available online at http://www.calfish.org/DataandMaps/tabid/88/Default.aspx), and groundtruthing to identify natural and artificial barriers to adult salmonids in the Scott River watershed.
Our assumption was that for successful fish passage to occur at a given site, the ratio of drop
height to pool depth must be greater than or equal to 1:1.5 or a minimum of 2 ft (0.6 m) depth
(Robison et al. 1999). We used estimated maximum jump height for Chinook salmon (12 ft;
3.67 m), coho salmon (4.82 ft; 1.47 m) and steelhead (3.47 ft; 1.03 m) (Meixler et al. 2009).
19
Physical Barriers in Scott River Watershed
Two natural and two man-made barriers were detected in the watershed (Figure 10).
Figure 10. Detected natural and man-made barriers to adult salmonid passage in Scott River Watershed.
Habitat Quality
Overall Results
Habitat types were delineated using high-resolution aerial photographs and field observations.
Between 24 August and 16 October 2009, we sampled 33 of 51 river sub-reaches (Figure 6).
Our sample sites represent ~1.4% (211m) of the total length of watershed channel (317021 m).
20
The Reaches sampled (218375 m) represent ~ 69% of the total watershed. This extrapolates to
~5,119,337 m2 (512 hectares; 1,245 acres) of active channel (mean channel width 19 m). Mean
channel widths ranged from 12 ft (4 m) at Moffett Creek (Reach 5) to 407 ft (124 m) at Scott
River (Reach 5). Mean stream gradients ranged from almost 0 at Kidder Creek (Reach 1) to 8.6
in Canyon Creek (Reach 1). Pool ratios ranged from 0.8 in Canyon Creek (Reach 2) to roughly 0
at Kidder Creek (Reach 1). Mean substrate particle size (pebble counts) ranged from 25.9 mm
(D50 = 7.1 mm) in Scott River Reach 2 to 287.2 mm (D50 = 145.5 mm) at Shackleford Creek
(Reach 4). Woody material coverage of surface area ranged from 0% at numerous locations to
3.3% at French Creek (Reach 3). Percent of fine substrate (< 9.5 mm diameter) by weight ranged
from 12.2% average at Kidder Creek (Reach 4) to 59.8% at Kidder Creek (Reach 5).
Figure 11. Identification of sampled and unsampled waters of the Scott River, July 2009 through July 2010.
21
Stream Habitat and Morphologic Mapping
In conjunction with surveying and sediment data collection morphologic mapping was
performed using criteria developed by Montgomery and Buffington (1997). The Montgomery
and Buffington (1997) classification is intended for reach scale morphologic mapping in
mountain drainage basins that delineates dune-ripple, riffle-pool, step-pool, plane bed, and
cascade morphologies based on slope, material size, bed material patterns, confinement, and pool
spacing. For our surveys, each of these characteristics were recorded and entered into a database
and a primary and secondary classification was given. This information, in conjunction with
differences in gradient, percent of various channel unit types, stream confluences and channel
width and bankfull depth helped us refine study reaches of the mainstem Scott River and its
tributaries.
Results from Stream Habitat and Morphologic Mapping
Figure 12 shows the relationship between measured average stream slope and morphology. An
example of this is a number of cascade reaches that by slope would otherwise be classified as
step-pool or plane bed. Morphologic mapping of the Scott River Watershed illustrates known
general trends with slope except when potential anthropogenic disturbances disrupt natural water
and sediment properties. Typically, riffle-pool and plane bed reaches are most susceptible to
watershed disturbances that impact the supply of water, sediment, or wood. Step-pool and
cascade reaches can exhibit a response to watershed impacts as well, but typically not as
pronounced (Montgomery and Buffington, 1997).
Potential sampling bias could have also skewed morphologic mapping because site access was
limited to sites with a close proximity to roads, indicating a potential legacy of anthropogenic
disturbances. For example, Etna Reach 2 was classified as cascade due to the random spatial
pattern of large boulders and weak proto-steps developing. Notably, this reach was upstream of
a man-made crossing that likely affected (or forced) the stream morphology by controlling the
downstream slope. Without the crossing the reach would likely be a step-pool morphology. A
natural anomaly is found in Kidder Creek Reach 4, where a band of bedrock created a local slope
control at the study reach. The reach was classified again as cascade due to the presence of
random boulders and intermittent steps. Upstream of this reach, gradient appeared to be in
excess of 4%.
22
0.06
0.05
Slope (ft/ft)
0.04
0.03
0.02
0.01
0.00
Cascade (n=11)
Step Pool (n=2)
Plane Bed (n=3)
Riffle Pool (n=17)
Morphology
Figure 12. Relationship between channel morphology and reach averaged gradient sampled in the Scott
River Watershed, California. Squares = mean; Whiskers = min and max.
Pool-Riffle Spawning Ground Sustainability
For alluvial reaches with non-forced morphologies, we utilized a metric for riffle and pool
sustainability that relates variations in the channel width to variations in the bed topography for
riffle and pool cross sections (Caamano et al. 2009). The equation, (BR/BP) – 1 = (DZ/HR) is
used as a threshold for a velocity convergence between pools and riffles to occur, implying
maintenance of form (BR = riffle width at bankfull, BP = pool width at bankfull, DZ = residual
pool depth, HR = bankfull riffle depth).
Alluvial reaches that were single thread and did not have forced pools were filtered from our
total data set and evaluated for sustainability. These reaches include the mainstem Scott River
reaches 1, 2, 3, 4, and 5, Moffett Creek reaches 4 and 5, French Creek reach 1, Patterson Creek
reach 1, and Shackleford Creek reach 1.
Results from Assessment of Pool-Riffle Spawning Ground Sustainability
Results suggest that all of the reaches analyzed except one (Moffett Creek reach 5) are
sustainable based on their geometry (Figure 13). While many of these sites are considered
“sustainable”, the results highlight that pool depths could be enhanced in confined reaches by
selectively widening riffle areas promoting greater flow divergence over riffle crests and
subsequent convergence in downstream pools. Alternatively, channel complexity and pool
volumes could be enhanced through the use of instream wood structures. This would be a
temporary fix unless a conjunctive riparian corridor restoration plan is developed.
Quantifying Substrate Quality
Bed Substrate Quality
We used both surface and subsurface grain size distributions to characterize the substrate.
According to Kondolf (2000), two key environmental parameters are of interest when assessing
the quality of streambed material for salmonid spawning:
23
(1) The size of the framework gravels (the larger gravels that make up the structure of the
deposit) is needed to assess whether gravels are small enough to be moved by a given salmonid
when constructing a redd. (2) The level of interstitial fine sediments which cannot be so high as
to interfere with incubation or emergence.
3
2.5
Unsustainable
DZ/HR
2
1.5
1
Sustainable
0.5
0
0
0.5
1
1.5
2
2.5
3
(BR/BP) -1
Figure 13. Sustainability of riffle pool units studied.
Surface Samples
For the surface samples, pebble counts were collected at 4 – 10 (mean 6) randomly selected
transects (~100 samples per transect) at each site using methods similar to those of Bauer and
Burton (1993). Surveyors collected substrate samples by hand every 1 ft (~0.3 m) along
transects and used a template to measure substrate size. Substrate from pebble counts were
categorized into 12 sizes: <8.0 mm, 8.0 mm, 16.0 mm, 22.2 mm, 31.8 mm, 44.5 mm, 63.5 mm,
89.0 mm, 127.0 mm, 177.8 mm, 254.0 mm, and >254.0 mm. The categorization was based on
the largest slot (round hole with specified diameter) through which an individual pebble could
not be passed (Merz et al. 2006). These data were incorporated into the GIS database and map.
Table 5 provides the mean, D50 and D84 substrate size of the pebble counts, percent wood and
percent exposed bedrock for the sampled reaches.
Subsurface Fine Sediment
At designated sites, 2 – 8 (mean 4) subsurface (core) samples were collected using a McNeil core
sampler (St-Hilaire et al. 1997). In the field, substrates were sieved through screens of the
following sizes: 9.5 mm; 12.7 mm; 16.0 mm; 22.2 mm; 31.8 mm; 44.5 mm; 63.5 mm; 88.9 mm;
127.0 mm; 177.8 mm; and, 254.0 mm. Each size-class was weighed and data recorded. Material
smaller than 9.5 mm and residual water were retained, and then transported to the lab for further
analysis. This material was separated out to size classes smaller than 9.50 mm and percentage
smaller than 0.85 mm because of their effect on embryo development, survival, and fry
emergence (Tappel and Bjornn 1983). Size classes were dried at 70°C for 24 h, weighed and
24
data recorded. Table 7 has the percent by weight of substrate less than 9.5 mm and 0.85mm
from the core samples in the sampled reaches.
Results from Substrate sampling
Table 5. Results of pebble counts and core samples within the Scott River Watershed.
Site
Stream
Reach
Province
Mean Substrate
(mm)
D50mm
D84mm
Percent
<9.5
Percent
<0.85
Percent
Wood
Percent
Bedrock
1
Canyon Creek
1
Canyon
200
68
345
15.7
1.7
0.3
0.0
2
Canyon Creek
2
Canyon
240
54
434
13.6
3.4
0.4
9.1
4
Crater Creek
1
South East
94
56
149
17.0
3.1
0.9
0.0
9
Etna Creek
1
West Side Granitic
58
36
66
25.6
8.2
1.6
0.0
10
Etna Creek
2
West Side Granitic
210
62
196
22.2
3.2
0.5
0.0
12
French Creek
1
West Side Granitic
81
50
85
20.8
5.3
1.6
0.0
13
French Creek
2
West Side Granitic
97
38
142
25.1
8.0
1.7
1.0
14
French Creek
3
West Side Granitic
123
61
146
17.0
2.8
3.3
18.5
15
French Creek
4
West Side Granitic
137
79
192
21.2
5.0
3.1
0.0
16
Grouse Creek
1
South East
139
46
215
32.6
6.7
0.0
19.0
18
Kidder Creek
1
West Side Non-Granitic
32
18
38
40.6
14.8
1.6
0.0
19
Kidder Creek
2
West Side Non-Granitic
48
29
59
31.9
13.1
0.0
0.0
21
Kidder Creek
4
West Side Non-Granitic
124
66
262
12.2
1.7
0.6
0.0
22
Kidder Creek
5
West Side Non-Granitic
198
73
374
59.8
17.0
0.0
12.1
25
Moffett Creek
3
East Side
71
17
115
41.1
12.1
0.0
1.5
26
Moffett Creek
4
East Side
31
19
40
46.7
15.0
0.6
0.0
27
Moffett Creek
5
East Side
46
29
59
31.9
12.8
0.6
0.0
31
Patterson Creek
1
West Side Non-Granitic
55
31
71
30.5
10.2
0.3
0.0
32
Patterson Creek
2
West Side Non-Granitic
83
46
350
31.1
7.9
0.3
0.0
35
S. Fork Scott River
2
South West
110
99
148
17.5
3.5
0.0
0.0
36
S. Fork Scott River
3
South West
241
82
433
13.3
2.0
0.6
22.1
37
S. Fork Scott River
4
South West
121
64
195
18.0
3.4
1.3
0.7
38
Scott River
1
Mainstem
159
5
79
47.5
16.0
1.2
16.0
39
Scott River
2
Mainstem
26
7
20
58.8
20.4
2.1
0.0
40
Scott River
3
Mainstem
37
25
32
42.6
14.7
0.0
0.0
41
Scott River
4
Mainstem
58
38
65
30.5
9.2
0.0
0.0
42
Scott River
5
Mainstem
93
62
109
21.1
6.6
0.0
0.0
43
Shackleford Creek
1
West Side Non-Granitic
62
35
74
27.1
6.9
0.3
0.0
44
Shackleford Creek
2
West Side Non-Granitic
192
71
367
19.2
4.2
1.3
0.0
45
Shackleford Creek
3
West Side Non-Granitic
82
35
89
49.9
9.4
0.0
41.5
46
Shackleford Creek
4
West Side Non-Granitic
287
145
463
22.1
3.7
0.3
0.0
49
Tompkins Creek
1
Canyon
110
70
154
17.4
4.8
1.9
0.0
50
Tompkins Creek
2
Canyon
100
43
145
21.1
3.1
2.3
0.0
25
Spawning Gravel Quality
We assessed gravel quality to determine how well the composition of existing substrates
compared to species-specific requirements for substrate size. In general, spawning females
excavate gravel to create a substrate bed depression, but not all material needs to be mobilized,
just ample amounts to construct the redd. Spawning will not be successful if adequate amounts
of gravel-sized material cannot be mobilized. In salmonids, fish size is directly proportional to
maximum movable substrate size, and can be used to effectively determine upper, speciesspecific size limit criteria for suitable spawning gravels. Kondolf (2000) describes a method for
determining appropriate spawning substrate size of a population whereby the maximum movable
substrate size for spawning female salmonids was defined as 10% of the average female’s length
(Figure 14). We used sex and fork length (mm FL) data collected from post-spawn coho salmon
in the Scott River watershed (unpublished data provided by SQRCD) to calculate the average
female size, and used 10% of the average female’s FL as the values to define the maximum
movable material size for this population. We also used FL frequency distributions to calculate
10% FL50 and FL84 values. All escapement data provided were collected between 16 November
2004 and 17 January 2005. Mean, FL50 and FL84 values were compared against existing
substrate conditions to determine habitat suitability indices. Specifically, substrate D50 and D84
were used to evaluate the suitability of existing spawning habitat and identify the potential for
restoration in different mainstem and tributary reaches throughout the watershed.
Results from Spawning Gravel Quality Assessment – Appropriate size classes for Scott
River coho salmon
Female coho salmon FL ranged from 540 to 830 mm FL with a mean of Mean 676 mm FL +/0.3 SE for the Scott River watershed. Median (FL50) length was 671 mm FL while FL84 was 728
mm FL (Figure 14). The corresponding values for 10 % mean FL, FL50, and FL84 to define and
assess the suitability of maximum movable substrate sizes were 67.6 mm, 67.1 mm, and 72.8
mm, respectively.
26
0.20
0.18
0.16
0.14
0.12
0.10
0.08
0.06
0.04
0.02
0.00
500 520 540 560 580 600 620 640 660 680 700 720 740 760 780 800 820 840 860 880 900
Female FL (mm)
Figure 14. Proportional distribution of female coho salmon fork length (mm FL) in the Scott River
watershed. All data collected between 16 November 2004 and 17 January 2005.
Because substrate size classes less than 9.5 mm have been associated with lower salmonid
embryo survival (Tappel and Bjornn 1983), these size classes were removed from the gravel
mixture (i.e. 4 and 8 mm). In their place, we increased the percent (by number) of material in the
next three larger size classes (i.e. 16 – 32 mm) proportionally to what was removed. In this way,
we provided a complex mixture of coarse sediment that could be utilize by the majority of the
spawning female population while avoiding potentially detrimental size classes for coho
embryos (Table 6).
Table 6. Recommended gravel mixture for Scott River coho salmon spawning.
Diameter
(mm)
4
8
16
22
32
44
64
76
89
127
178
Percent of
population
0
0
18
26
24
20
5
5
1
0.5
0.5
27
Figure 15. Gravel composition (D50) in the Scott River watershed; data provided by pebble count surveys
Embryo Survival Model
We used the results from Tappel and Bjornn (1983) to build a regression model of salmon
embryo survival to percent substrate smaller than 9.50 mm and 0.85 mm (Figure 16). We then
input the proportion of substrate smaller than 9.50 mm and 0.85 mm at each of our sample
locations into the model to predict salmon embryo survival.
28
Estimated percent embryo survival
Estim ated percent embryo susrvival
0.85 mm
100
80
y = -0.1474x2 - 2.0339x + 98.248
R2 = 0.8901
60
40
20
0
0
5
10
15
20
25
Proportion of substrate less than 0.85 mm
Estim ated percent em bryo survival
9.5 mm
100
2
y = -0.0417x + 0.6775x + 100
2
R = 0.8089
80
60
40
20
0
0
10
20
30
40
50
60
Proportion of substrate less than 9.5 mm
Figure 16. The relationship between substrate size classes (0.85 and 9.5 mm) and salmon embryo survival.
Data taken from Tappel and Bjornn (1983) to build regression models).
Results from Embryo Survival Model
Fines known to affect Pacific salmon embryo survival ranged from just under 2% to nearly 60%
of bed substrate within reaches accessible to anadromous salmonids (Table 7). Modeled embryo
survival to emergence (Figure 17) ranged from 0 to 95% survival, assuming all other physical
requirements were met (e.g., flow, temperature, disease).
29
Table 7. The estimated relative survival of salmon embryos in relationship to fine sediment in the Scott River
watershed, California.
Site
12.2
1.7
100
95
21
Kidder Creek
4
1
1
Canyon
15.7
1.7
100
95
36
Canyon Creek
S. Fork Scott
River
3
13.3
2.0
100
94
14
French Creek
3
South West
West Side
Granitic
17.0
2.8
99
92
2
Canyon Creek
2
Canyon
13.6
3.4
100
90
4
Crater Creek
S. Fork Scott
River
S. Fork Scott
River
Tompkins
Creek
1
South East
17.0
3.1
99
91
2
South West
17.5
3.5
99
90
4
South West
18.0
3.4
99
90
2
21.1
3.1
96
91
2
22.2
3.2
95
90
19.2
4.2
98
87
4.8
99
85
22.1
3.7
95
89
15
French Creek
4
21.2
5.0
96
85
12
French Creek
1
Canyon
West Side NonGranitic
West Side
Granitic
West Side
Granitic
17.4
46
Etna Creek
Shackleford
Creek
Tompkins
Creek
Shackleford
Creek
Canyon
West Side
Granitic
West Side NonGranitic
20.8
5.3
96
84
42
5
6.6
96
78
27.1
6.9
88
77
13
French Creek
2
25.1
8.0
91
72
9
Etna Creek
1
n/a
West Side NonGranitic
West Side
Granitic
West Side
Granitic
21.1
43
Scott River
Shackleford
Creek
25.6
8.2
90
72
16
Grouse Creek
Patterson
Creek
1
South East
West Side NonGranitic
32.6
6.7
78
78
31.1
7.9
81
73
4
n/a
West Side NonGranitic
30.5
9.2
82
67
31
Scott River
Patterson
Creek
30.5
10.2
82
62
27
Moffett Creek
5
31.9
12.8
79
48
19
Kidder Creek
2
East Side
West Side NonGranitic
31.9
13.1
80
46
25
3
12.1
58
52
49.9
9.4
30
66
18
Kidder Creek
1
East Side
West Side NonGranitic
West Side NonGranitic
41.1
45
Moffett Creek
Shackleford
Creek
40.6
14.8
59
36
40
Scott River
3
n/a
42.6
14.7
53
37
26
Moffett Creek
4
East Side
46.7
15.0
41
35
38
Scott River
1
47.5
16.0
38
28
22
Kidder Creek
5
n/a
West Side NonGranitic
59.8
17.0
0
21
39
Scott River
2
n/a
58.8
20.4
0
0
0-25%
25-50%
51-75%
76-100%
37
50
10
44
49
32
41
Reach
Percent
<85mm
Province
West Side NonGranitic
35
Stream
9.5 mm
0.85 mm
Estimated % Estimated %
survival
survival
Percent <
9.5mm
2
1
4
1
2
1
3
Colors indicates estimated survival of salmon
embryos in relationship to percent fines
30
Figure 17. Results of embryo survival model with survival to emergence in the Scott River watershed.
31
Quantify Gravel Mobility Rates
Overall Approach
Our approach to estimating sediment transport was tailored to the scope of the watershed
assessment and the life history requirements of the focal species. Rather than attempt to obtain
“absolute” sediment transport data, which is notoriously stochastic in time and space, we took a
relativistic approach. This approach utilizes variables that intrinsically control the transport and
storage of sediment in rivers and streams (Parker et al. 1998) while allowing intra-comparisons
amongst study reaches.
Three basic methods were employed using collected field data (slope, morphology, sediment
sizes, etc). Further we employed a regional regression for estimated streamflow based on
instrinsic basin properties to assess streamflows with the basin consistently. We determined the
potential transport capacity of the existing sediment size distribution as well as for an ideal
“Coho mix” to understand which reaches have a strong likelihood of transporting or storing
existing and potentially augmented gravels. We also utilized a sediment supply index that relates
predicted to actual gravel sizes to understand which reaches are supply or transport limited.
Lastly, we performed an annual assessment of potential redd scour at appropriate study reaches
to understand survival of embryos.
At-a-Station Sediment and Transport Capacity Analysis
Gravel mobility was assessed using field based sampling and at-a-station empirical estimates of
relative sediment supply and transport capacity. Cross section, channel slope, peak discharge
estimates and grain size data were used in the Bedload Assessment for Gravel-bed Streams
(BAGS) program (Pitlick et al. 2009) to estimate potential sediment transport capacities in the
study reaches. For this analysis, the Parker (1990) and Wilcock and Crowe (2003) sediment
transport relationships for bedload transport in gravel-bed rivers were utilized. Two discharges
were utilized for all simulations, the 2- and 100-year flows.
Estimation of Peak Runoff
By determining peak runoff, we assessed sediment transport basin-wide. Peak runoff was
determined for the 2, 5, 10, 25, 50, and 100-year recurrence intervals at each study site using
regression equations developed for the State of California (Waananen and Crippen 1977; Table
8). The regression equations require drainage area, mean annual precipitation (MAP), and an
altitude index. The drainage area for each site was digitized in ArcGISTM manually using data
from 7.5 min. USGS topographic maps. Mean annual precipitation was derived from from the
2009 PRISM rainfall data set for California. For each drainage area, the area of each isohyetal
was measured and a weighted MAP value was determined. It is noted that the regression
equations used in this study can have as much as 50% error (Mann et al. 2004). Typically, this
error leads to underestimated peak discharges and decreases with recurrence interval (Mann et al.
2004). Because our primary use of these discharges is to estimate sediment transport capacity,
we accept this method as a means to rapidly assess study reaches within the Scott River basin.
32
Results of Estimation of Peak Runoff
Table 8. Calculated peak runoff for study reaches within the Scott River Watershed, California.
Stream
Reach
Province
Canyon Creek
Canyon Creek
Canyon Creek
Crater Creek
East Fork Scott River
East Fork Scott River
East Fork Scott River
East Fork Scott River
Etna Creek
Etna Creek
Etna Creek
French Creek
French Creek
French Creek
French Creek
Grouse Creek
Grouse Creek
Kidder Creek
Kidder Creek
Kidder Creek
Kidder Creek
Kidder Creek
Moffett Creek
Moffett Creek
Moffett Creek
Moffett Creek
Moffett Creek
Moffett Creek
Moffett Creek
Big Slough
Patterson Creek
Patterson Creek
Patterson Creek
S. Fork Scott River
S. Fork Scott River
S. Fork Scott River
S. Fork Scott River
Scott River
Scott River
Scott River
Scott River
1
2
3
1
1
2
3
4
1
2
3
1
2
3
4
1
2
1
2
3
4
5
1
2
3
4
5
6
7
1
1
2
3
1
2
3
4
1
2
3
4
Canyon
Canyon
Canyon
South East
South East
South East
South East
South East
West Side Granitic
West Side Granitic
West Side Granitic
West Side Granitic
West Side Granitic
West Side Granitic
West Side Granitic
South East
South East
West Side Non Granitic
West Side Non Granitic
West Side Non Granitic
West Side Non Granitic
West Side Non Granitic
East Side
East Side
East Side
East Side
East Side
East Side
East Side
West Side Non Granitic
West Side Non Granitic
West Side Non Granitic
West Side Non Granitic
South West
South West
South West
South West
Valley
Valley
Valley
Valley
Avg. Mean
Altitude
Annual
Area - A Precipitation - Index - H
3
(sq mi)
P (in)
(10 ft) Q2 (cfs)
25
64
3.9
1,359
20
68
4.44
1,105
NA
NA
NA
NA
3
50
6
139
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
27
47
3.9
1,096
20
52
4.4
895
NA
NA
NA
NA
31
32
4.62
814
22
36
4.7
663
13
37
4.88
420
4
39
5.26
145
6
51
4.94
279
NA
NA
NA
NA
29
49
3.915
1,218
27
51
3.97
1,185
NA
NA
NA
NA
23
55
4.26
1,046
17
61
4.58
868
NA
NA
NA
NA
NA
NA
NA
NA
70
29
3.635
1,742
59
30
3.815
1,514
32
33
3.97
914
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
13
42
3.855
534
12
44
4.18
473
NA
NA
NA
NA
NA
NA
NA
NA
27
43
4.74
939
18
45
5.08
650
4
52
5.9
192
674
34
3.19
16,365
661
34
3.235
15,943
599
33
3.265
14,202
338
32
3.36
8,282
Q5
(cfs)
Q10
(cfs)
Q25
(cfs)
Q50
(cfs)
Q100
(cfs)
2,412
1,998
NA
265
NA
NA
NA
NA
1,931
1,607
NA
1,450
1,190
761
269
514
NA
2,147
2,095
NA
1,872
1,574
NA
NA
2,985
2,615
1,599
NA
NA
NA
943
846
NA
NA
1,690
1,185
362
27,071
26,421
23,572
13,871
3,487
2,928
NA
402
NA
NA
NA
NA
2,773
2,341
NA
2,092
1,728
1,115
402
765
NA
3,085
3,016
NA
2,721
2,311
NA
NA
4,181
3,685
2,279
NA
NA
NA
1,360
1,230
NA
NA
2,459
1,743
548
36,788
35,951
32,112
19,045
4,963
4,232
NA
609
NA
NA
NA
NA
3,932
3,371
NA
3,000
2,495
1,624
597
1,128
NA
4,374
4,286
NA
3,904
3,353
NA
NA
5,801
5,147
3,219
NA
NA
NA
1,936
1,770
NA
NA
3,551
2,545
826
49,324
48,278
43,194
25,837
6,840
5,907
NA
867
NA
NA
NA
NA
5,384
4,676
NA
4,139
3,455
2,259
837
1,580
NA
5,998
5,888
NA
5,405
4,684
NA
NA
7,816
6,971
4,382
NA
NA
NA
2,642
2,436
NA
NA
4,939
3,565
1,176
65,890
64,571
57,789
34,649
8,563
7,476
NA
1,121
NA
NA
NA
NA
6,720
5,898
NA
5,216
4,365
2,863
1,067
2,011
NA
7,492
7,365
NA
6,804
5,937
NA
NA
9,653
8,645
5,457
NA
NA
NA
3,291
3,055
NA
NA
6,254
4,543
1,519
80,650
79,122
70,846
42,571
Results from the At-a-Station Sediment and Transport Capacity Analysis
Results were normalized by the average bedload transport among all reaches to help with crosscomparisons between study sites (Figure 18 and Figure 19).
33
Scott River: Reach 4
Scott River: Reach 5
Shackleford Creek: Reach 1
Shackleford Creek: Reach 2
Shackleford Creek: Reach 3
Shackleford Creek: Reach 4
Tompkins Creek: Reach 1
Tompkins Creek: Reach 2
Scott River: Reach 3
Scott River: Reach 4
Scott River: Reach 5
Shackleford Creek: Reach 1
Shackleford Creek: Reach 2
Shackleford Creek: Reach 3
Shackleford Creek: Reach 4
Tompkins Creek: Reach 1
Tompkins Creek: Reach 2
Patterson Creek: Reach 2
S. Fork Scott River: Reach 2
S. Fork Scott River: Reach 3
S. Fork Scott River: Reach 4
Scott River: Reach 1
Scott River: Reach 2
Scott River: Reach 3
Scott River: Reach 2
Scott River: Reach 1
S. Fork Scott River: Reach 4
S. Fork Scott River: Reach 3
S. Fork Scott River: Reach 2
Patterson Creek: Reach 1
Moffett Creek: Reach 5
Moffett Creek: Reach 4
Moffett Creek: Reach 3
Kidder Creek: Reach 4
Grouse Creek: Reach 1
French Creek: Reach 4
French Creek: Reach 3
French Creek: Reach 2
French Creek: Reach 1
Etna Creek: Reach 2
Etna Creek: Reach 1
Crater Creek: Reach 1
Canyon Creek: Reach 2
Canyon Creek: Reach 1
34
Patterson Creek: Reach 2
Patterson Creek: Reach 1
Moffett Creek: Reach 5
Moffett Creek: Reach 4
Moffett Creek: Reach 3
Kidder Creek: Reach 4
Grouse Creek: Reach 1
French Creek: Reach 4
Q100 - Existing Pebble Distribution Transport Rate
6.0
French Creek: Reach 3
French Creek: Reach 2
French Creek: Reach 1
Etna Creek: Reach 2
Etna Creek: Reach 1
Crater Creek: Reach 1
Canyon Creek: Reach 2
Canyon Creek: Reach 1
4.0
3.0
2.0
1.0
Normalized Transport Capacity
4.5
4.0
3.5
3.0
2.5
2.0
1.5
1.0
Normalized Transport Capacity
Q2 - Existing pebble Distribution Transport Rate
6.0
5.5
5.0
0.5
0.0
5.0
0.0
Figure 18. Normalized average bedload transport among study reaches of the Scott River Watershed,
California.
Interpretation of Figure 19 is that study reaches with high transport capacity will likely evacuate
spawning gravels very rapidly at bankfull flows. Study reaches with low transport capacities
will have a higher probability of maintaining spawning gravels.
An ideal coho mixture of gravel was determined based on available fork length data. We used
this mixture to rank reaches based on their potential to maintain gravels needed for coho
spawning. This gravel mixture was evaluated for the 2 year event (Figure 19). We used this
mixture to rank reaches based on their potential to maintain gravels needed for coho spawning.
The ranking will be applied to potential sites that meet criteria for gravel augmentation as
discussed below.
5.0
Q2 - Coho Gravel Mixture Transport Rate
Normalized Transport Capacity
4.0
3.0
2.0
1.0
0.0
Tompkins Creek: Reach 2
Tompkins Creek: Reach 1
Shackleford Creek: Reach 4
Shackleford Creek: Reach 3
Shackleford Creek: Reach 2
Shackleford Creek: Reach 1
Scott River: Reach 5
Scott River: Reach 4
Scott River: Reach 3
Scott River: Reach 2
Scott River: Reach 1
S. Fork Scott River: Reach 4
S. Fork Scott River: Reach 3
S. Fork Scott River: Reach 2
Patterson Creek: Reach 2
Patterson Creek: Reach 1
Moffett Creek: Reach 5
Moffett Creek: Reach 4
Moffett Creek: Reach 3
Kidder Creek: Reach 4
Grouse Creek: Reach 1
French Creek: Reach 4
French Creek: Reach 3
French Creek: Reach 2
French Creek: Reach 1
Etna Creek: Reach 2
Etna Creek: Reach 1
Crater Creek: Reach 1
Canyon Creek: Reach 2
Canyon Creek: Reach 1
Figure 19. Estimated transport rate for coho-appropriate spawning gravel sizes per study reach.
Sediment Supply Index (SSI)
Determining the actual sediment supply at any given space and time in a river is difficult to
achieve with confidence as processes governing sediment transport are inevitably stochastic. To
assess the sediment supply of a study reach relative to all study sites we used a sediment supply
index based on the competent median particle size (D50) relative to the measured particle size for
bankfull flows (D50_C assumed to be Q2) scaled by the contributing drainage area. The data was
then normalized by the average drainage area to further illustrate relative supply. This approach
has been used previously by Buffington and Montgomery (1999) and Buffington et al. (2004) but
without drainage area scaling. The index takes the form:
SSI = ((D50C/ D50) • Drainage area)/ Average Drainage Area
35
Equilibrium bedload transport is typically represented as power function of excess shear stress so
it follows that it is also a power function of the competent and observed median grain sizes. In
this fashion surrogates for the applied and critical shear stresses are the observed and competent
grain sizes (Buffington and Montgomery 1999). The SSI ratio is a measure of sediment supply
incorporating sediment grain sizes observed versus what is theoretically stable at bankfull that is
also scaled and normalized by drainage area. When actual particle sizes are smaller than
predicted for equilibrium the first ratio will be greater than 1, indicating that sediment in excess
of that needed for equilibrium may persist at the study reach. A larger drainage area would
“scale” this ratio higher while a smaller one would reduce it. Conversely, when the actual
particle sizes are larger than predicted for equilibrium the first ratio will be less than 1, indicating
that sediment in excess of that needed for equilibrium would not persist at the study reach.
Results from the Sediment Supply Index
Our analysis indicates that the lower gradient reaches of the Scott River typically have higher
sediment supply relative to the size of the drainage area (higher SSI’s). This is consistent with
our understanding of watershed sediment dynamics (Figure 20). The excess of supply relative to
equilibrium conditions however, can be attributed to either intrinsic properties of the watershed
or study reach or from physical modifications to the stream geometry that prohibits particle
sorting.
7.5
7.0
6.5
Sediment Supply Index (SSI)
6.0
5.5
5.0
4.5
4.0
3.5
3.0
2.5
2.0
1.5
1.0
0.5
Figure 20. Sediment Supply Index for study reaches of Scott River Watershed, California.
36
Tompkins Creek 2
Tompkins Creek 1
Shackleford Creek 4
Shackleford Creek 3
Shackleford Creek 2
Scott River 5
Shackleford Creek 1
Scott River 4
Scott River 3
Scott River 2
Scott River 1
S. Fork Scott River 4
S. Fork Scott River 3
Patterson Creek 2
S. Fork Scott River 2
Moffett Creek 5
Patterson Creek 1
Moffett Creek 4
Kidder Creek 5
Moffett Creek 3
Kidder Creek 3
Kidder Creek 2
Kidder Creek 1
French Creek 4
Grouse Creek 1
French Creek 3
French Creek 2
Etna Creek 2
French Creek 1
Etna Creek 1
Crater Creek 1
Canyon Creek 2
Canyon Creek 1
0.0
Risk of Redd Scour Analysis
We classified the risk of redd scour at selected spawning grounds using published data on
hydraulic and sediment transport conditions known to impact salmonid redds (May et al. 2007).
We determined the times salmonids spawn in the basin and identified when salmonid eggs are
incubating with the range of water depths expected. Using flow data and sediment transport
scour core data, we determined the range of flows that may be expected during the egg
incubation period and determined the thresholds for redd scouring in each of the study reaches.
We developed a map delineating zones of possible redd scour risk.
Depth of Scour Analysis
For this aspect of the study we wanted to relate maximum annual scour depths with depths of
egg burial depths for coho salmon. Contemporary thinking is that egg burial depths coincide
with typical disturbance depths from sediment mobilization (Montgomery et al. 1996; Buffington
et al. 2004). For example, DeVries (2002) found annual disturbance depths to be 1.5 times the
D90. Changes in sediment supply or discharge can alter this regime and increase the risk of redd
scour to salmonids.
For spawning and incubation timing, we used a combination of information from carcass and
redd surveys performed on the Scott River (Maurer 2002; Quigley 2005) and overall timing for
coho of the Pacific Southwest, including the Klamath Watershed (Hassler 1987; Weitkamp et al.
1995).
For range of depths for expected incubation, we used fork length data from coho salmon carcass
surveys performed on the Scott River (e.g. Quigley 2005) and the calculation of nest depth as a
function of female coho size from van den Berghe and Gross (1984). From those data, we
estimated redd depth relationship to female fork length as:
y = -10.44 + 0.411x
Where
y = Redd Depth
x = Female Length
A sliding bead monitor with a machined end point was used to measure in situ scour depths
(Nawa and Frissel 1993) through the 2010 water year (Figure 21). Installations occurred in
September and October 2009 during low flow and/or dry conditions. Because we had to move
the surface layer in some cases to install the scour chains, we added the median particle size to
the total scour depth. This is because subsurface scour of the beads cannot occur unless the
surface is mobilized.
37
Figure 21. An example of the Scour chains used to determine sediment mobility.
Results from Risk of Redd Scour Analysis
Timing
Coho have been observed spawning between 1 November and 15 January. The amount of time it
takes for embryos to hatch and emerge is strongly related to temperature and to a lesser extent
oxygen (see Sandercock 1991). In the United States, coho embryos may take anywhere from 3856 days to hatch with another 21 to 40 days further to hatch. This suggests embryos should be
incubating in the gravel between 1 November and 15 April with a conservative estimate of all fry
emerging by 15 May (Figure 22). Therefore, scour chains were installed and operated from early
October 2009 to the first week of July 2010.
38
Month
Fall-Run Chinook
January
February
March
April
May
June
July
August
Adult Migration and Holding
September
October
October 15 - December 31
October 15 - March 15
Fry Emergence
Coho
October 15 - March 15
January 1 - April 15
January
February
March
April
May
June
July
August
Adult Migration and Holding
Spawning
Embryo Incubation
Fry Emergence
December
August 1 - December 31
Spawning
Embryo Incubation
November
September
October
November
December
September 1 - December 31
Nov 1 - Jan15
November 1 - January 15
November 1 - April 15
November 1 - April 15
February 1 - May 15
adapted from Trinity River Salmonid Life-History Table available at http://www.trrp.net/TrinityRiver/fishresources.htm; Trinity River Flow Evaluation - Final Report. 1999. A Report to the Secretary, U.S. Department of the Interior, Washington, D.C. prepared by the
U.S. Fish and Wildlife Service, Arcata Fish and Wildlife Office, Arcata, CA and the Hoopa Valley Tribe, Hoopa, CA. 513 pages; Maurer (2002) and Quigley (2005)
Figure 22. Estimated timing of Chinook and coho salmon spawning and incubation for the Scott River, CA.
39
Fish Size and Redd Depths
Female coho salmon in the Scott River have ranged from 55 – 85 cm FL (Figure 23). This
suggests redd depths are from 13 – 24 cm (Table 9). Therefore, we assume scour that exceeds a
depth of 13 mm from 1 November through 15 May is potentially detrimental to Scott River coho
redds (Figure 24). Note: Measurements of the redd “pit” (egg pocket) were performed on
completed redds during the coho spawning surveys of 2004-05 (Quigley 2005). An average
excavation depth of 19.5 cm was measured on all tributaries on a total of over 530 redds. These
empirical values correlate well with the values derived from the FL analysis.
Female coho forklength
35%
30%
Percent observed
25%
20%
15%
10%
5%
0%
52
56
60
64
68
72
76
80
84
88
92
96
FL (cm)
Figure 23. Length frequency of female coho salmon observed during carcass surveys of the Scott River,
California. Data from SQRCD surveys.
Table 9. Estimated redd depths for coho salmon length frequencies observed in the Scott River, California.
As a
Redd depth By number proportion of
(cm)
of females population
12.6
14.2
15.9
17.5
19.2
20.8
22.4
24.1
6
6
63
81
103
48
8
1
2%
2%
20%
26%
33%
15%
3%
0%
40
100
35%
redd depths
30%
Percent of observed
25%
20%
15%
10%
5%
0%
10
13
14
16
18
19
21
22
24
26
Redd depths (cm)
Figure 24. Estimated redd depths for coho salmon length frequencies for Scott River, California.
Scour Cores
An attempt was made to insert a scour monitor at every study site, but large boulders and the
presence of shallow bedrock limited the study to selected reaches where the scour monitors could
actually be inserted. A total of 23 scour chains were installed throughout the Scott River
Watershed October 2009 (Table 10). A total of 15 chains were recovered between 12 and 13
July 2010.
Table 10. Information on scour chain stations installed throughout the Scott River Watershed October 2009 and
recovered July 2010
Id
Stream
4
Crater Creek
Reach1
Feature
Scour Depth
(cm)
Deposition (cm)
Scour beads
4.8
0
Y
X
9
Etna Creek
1
Scour beads
NR
NR
41.4703121390
-122.8574434798
12
French Creek
1
Scour beads
7.2
8
41.3957368675
-122.8713009318
13
French Creek
2
Scour beads
NR
NR
41.3860021305
-122.8754536723
16
Grouse Creek
1
Scour beads
8.4
0
41.3167458394
-122.6985592305
25
Moffett Creek
3
Scour beads
0
0
41.6334397589
-122.7403538394
26
Moffett Creek
4
Scour beads
2.4
3
41.5922933271
-122.7270788565
27
Moffett Creek
5
Scour beads
0
0
41.5799179475
-122.7087572847
31
Patterson Creek
1
Scour beads
0
3
41.5058487986
-122.8980437702
32
Patterson Creek
2
Scour beads
2.4
10
41.5093759055
-122.9328257132
35
S. Fork Scott River
2
Scour beads
2.4
0
41.2890999271
-122.8389962684
38
Scott River
1
Scour beads
10.8
8
41.6358686409
-123.0785131343
38
Scott River
1
Scour beads
NR
NR
41.6358764545
-123.0784060841
38
Scott River
1
Scour beads
NR
NR
41.6406481014
-123.0150965569
38
Scott River
1
Scour beads
NR
NR
41.6406235930
-123.0151035750
39
Scott River
2
Scour beads
NR
NR
41.5676577972
-122.8464386444
39
Scott River
2
Scour beads
21.6
8
41.6336828025
-122.9602726435
39
Scott River
2
Scour beads
NR
NR
41.6336773146
-122.9602690012
40
Scott River
3
Scour beads
0
0
41.4756476383
-122.8492228340
41
Scott River
4
Scour beads
6
0
41.4213235496
-122.8448798583
42
Scott River
5
Scour beads
NR
NR
41.3439707135
-122.8251360287
43
Shackleford Creek
1
Scour beads
3.6
13
41.6216413582
-122.9655781026
44
Shackleford Creek
2
Scour beads
2.4
33
41.5933019809
-122.9910726449
41
Only one monitoring site – on the mainstem Scott River Reach 2 – had scour that exceeded the
upper boundary for Coho redds during the 2009-2010 spawning and incubation period. It is
difficult to extrapolate meaning based on results from one year of monitoring. Considering that
the effort for scour chain installation is moderate, future monitoring should be performed through
a variety of water year types.
Sampling of Woody Material
We took length and diameter breast height (DBH) estimates on a subset of woody material
observed during surveys of the Scott River Watershed (material with diameter greater than 3
inches). We then estimated the volume of wood per piece by the following formula:
Cubic foot = (DBH/2)2 • 3.1415 • Height • 0.7
Board foot = (DBH/2)2 • 3.1415 • Height • 0.7 • 12
Results from Woody Material Sampling
A total of 28 wood pieces were measure for volume estimation. Average material length was 30
ft (9.1m) and width 1.3 ft (Table 11). For the Scott River mean wood volume for individual
pieces was 53 ft3 (min 1.03; Max 209.4) (1.5 m3). The number of woody pieces observed within
the study reaches ranged from 0 to 3.3 per 100 m (328 ft). We estimated that the entire Scott
River watershed averaged 0.88 pieces per 100 m (Figure 25). Over half of the documented wood
pieces were located in three reaches: Tompkins Creek 1 (n=8), Tompkins Creek 2 (n=5) and
Patterson Creek 2 (n =5). Woody material was documented in only eight of the thirty three
reaches sampled.
Table 11. Estimation of LWM from sampled reaches of the Scott River watershed.
ID
Stream
Reach
Count
DBH
(ft)
4
15
15
16
18
18
18
18
18
32
32
32
37
49
49
49
49
49
49
49
49
50
50
50
50
50
Crater Creek
French Creek
French Creek
Grouse Creek
Kidder Creek
Kidder Creek
Kidder Creek
Kidder Creek
Kidder Creek
Patterson Creek
Patterson Creek
Patterson Creek
S. Fork Scott River
Tompkins Creek
Tompkins Creek
Tompkins Creek
Tompkins Creek
Tompkins Creek
Tompkins Creek
Tompkins Creek
Tompkins Creek
Tompkins Creek
Tompkins Creek
Tompkins Creek
Tompkins Creek
Tompkins Creek
1
4
4
1
1
1
1
1
1
2
2
2
4
1
1
1
1
1
1
1
1
2
2
2
2
2
1
1
1
1
1
1
1
1
1
3
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0.4
2.0
0.6
4.0
1.7
1.2
2.0
1.0
0.7
3.6
2.0
0.7
1.2
1.3
1.5
0.5
0.8
1.0
0.8
2.0
2.0
0.3
1.5
0.3
0.3
0.3
Estimated
Length Debris Vol
3
(ft)
(ft )
5
20
10
10
22
26
26
16
18
89
62
35
4
35
60
30
25
12
50
80
20
20
20
30
30
30
0.5
44.0
1.9
88.0
33.6
20.9
57.2
8.8
4.4
209.4
136.3
8.6
3.0
34.2
74.2
4.1
9.5
6.6
19.1
175.9
44.0
1.2
24.7
1.0
1.0
1.0
Estimated
Debris
Volume
(board ft)
5.7
527.8
22.4
1055.5
403.2
250.4
686.1
105.6
52.8
2513.0
1636.1
102.6
35.9
410.5
890.6
49.5
114.5
79.2
229.1
2111.1
527.8
14.7
296.9
12.4
12.4
12.4
42
Photo Comment
Yes
partially embedded and decomposing in right bank
Yes
Yes
Yes
Yes
Yes
Bedrock section, LWD may not contribut to forced feature
Yes
Yes
Yes
double tree, embedded rootwad, combined DBH
embedded rootwad with tree
embedded rootwad and main trunk
overhanging log jam
Three logs stack, DBH represents combined diameters
Transverse jam, good feature
Alder
Figure 25. Density (percent surface area coverage) of woody material (>3 in diameter) within study reaches of
the Scott River
43
Identify Quantity and Quality of Potential Spawning Habitat Watershed Wide
Habitat Model Description and Output
Using an integration of the data analysis described above, we have developed the following
information evaluation process used to identify and prioritize watershed reaches for potential
gravel augmentation and structural enhancement sites in the Scott River Watershed (Charts 1;
Figure 26). The approach is described here, and then applied in the next section to develop a
series of sites and recommended actions.
Chart 1. Prioritization of Coho Spawning Habitat
What is the time that stream sections are open to adult fish during spawning season?
Data missing
~ 25%
~ 50%
Low Priority
A
~ 75 – 100%
Medium Priority
High Priority
Evaluate and if appropriate fix
Evaluate and if appropriate fix
No
Yes
Is the barrier natural?
Is there a physical barrier to
fish passage?
Yes
Implement
additional
monitoring and
reassess
(e.g. >4 or sediment
torrent overwhelms
channel)
No
No
Is the stream gradient appropriate for spawning?
< 1%
Reach inappropriate;
No further evaluation
needed
Yes
1 – 3%
Medium Priority
Low Priority
D
What is the dominant substrate?
Bedrock
Yes
C
3 – 4%
High Priority
Yes
Generally
meets
spawning
requirements;
go to Chart 2
B
No
D50 > 256 mm
No
Yes
D50 < 8 mm
No
Figure 26. Prioritization of coho salmon spawning habitat.
Habitat Accessibility (A and B)
In order for streams to be considered for spawning habitat, they must be physically accessible to
fish. That is, they must open (flow) at the appropriate time for target salmonids to use them;
habitat must connect to waterways further downstream at times when adults are migrating
upstream and during the spawning season. Secondly, fish must be able to physically surmount
obstacles within the watershed during migration to potential habitat and remain healthy enough
to complete their life cycle.
A.
Timing of Stream Opening
Described in detail above, we used weir counts and redd and carcass survey reports to identify
adult timing of coho and Chinook salmon. We then used flow data for our primary stream
44
reaches along with field surveys to identify when each of these reaches became connected to the
lower system (Chart 1).
B.
Physical Barriers
For this evaluation, we used data from Calfish, a collaborative website that provides access to
anadromous fish datasets (e.g., anadromous abundance, barriers, and restoration Projects) to
identify natural and artificial barriers to adult salmonids in the Scott River watershed:
http://www.calfish.org/DataandMaps/tabid/88/Default.aspx
We then ground-truthed identified sites.
Our assumption was that for successful fish passage to occur at a given site, the ratio of drop
height to pool depth is greater than or equal to 1:1.5 or a minimum of 0.6 m (2 ft) depth
(Robison et al. 1999). We used estimated maximum jump height Chinook salmon (3.67 m),
coho salmon and steelhead (1.47 m) (Meixler et al. 2009).
C.
Stream Gradient and Salmonid Spawning Habitat
It is generally accepted that Pacific salmon spawn and rear in stream reaches with a gradient
(slope) less than 4-5% (Lunetta et al. 1997). We used the gradient preferences (Table 12) set
forth by Montgomery et al. (1999) to classify stream reaches for spawning salmonids.
Montgomery and Buffington (1997) proposed a geomorphically based channel classification
system and identified five alluvial channel types based on slope, substrate, roughness elements,
confinement, and pool spacing including:

cascade (8.0 – 30.0% slope)

step-pool (3.0 – 8.0% slope)

plane-bed (1.0-4.0% slope)

pool-riffle (0.1-2% slope), and

dune-ripple/regime (<0.1% slope).
According to Roni et al. (1999), this channel-classification scheme allows for adjustment of
channel type due to morphological influences of large wood material and other elements and has
been used to define habitat use for juvenile and adult Pacific salmon (Inuoue et al 1997; Lunetta
et al. 1997). For example, spawning coho and Chinook salmon densities are generally low in
plane-bed channels, highest in pool-riffle and forced-pool-riffle channels, and virtually absent in
steeper channels (Table 13) (Buffington et al. 1999). Pool-riffle and forced-pool-riffle channels
also appear to represent areas of high-quality rearing habitat for juvenile salmonids (Inoue et al.
1997; Lunetta et al. 1997). Stream reaches of greater than 4% slope are generally not utilized by
Pacific salmon for spawning because of the reaches’ high bed load transport rate, deep scour, and
coarse substrate (Buffington et al. 1999). Initially, stream reaches with slopes less than 4% can
be identified using GIS technology or topographic maps and available stream survey data
45
(Lunetta et al. 1997; Roni et al. 1999). However, channel types identified with GIS technology
can differ from those actually present in the field (Lunetta et al. 1997; Montgomery and
Buffington 1997). Therefore, it is important that 1:24,000- or larger-scale maps are used to
determine potential channel type and a fine-scale (30m or less) digital elevation model be used to
calculate slopes. Further, slope and channel type should be confirmed by site visits in a
representative number of reaches or with existing habitat surveys (Roni et al. 1999).
Table 12. Relative priority of channel gradient for spawning by Chinook and coho salmon (Montgomery et al.
1999).
Species
Chinook
Coho
Gradient
<0.01 0.01-0.030.03-0.04 >0.04
High
Low
None
None
Medium High
Low
None
Table 13. Relative use of four primary stream habitats by Chinook and coho salmon (Buffington et al. 1999).
Species
Chinook
Coho
step-pool
None
Very Low
pool-riffle
High
Medium
forced poolriffle
High
High
plane bed
None
Low
D.
Evaluate Dominant Substrate Appropriateness for Spawning
We assessed gravel quality to determine how well the particle (or sediment) size distributions of
existing substrates compare to species-specific requirements for substrate size. In general,
spawning females excavate gravel to create a substrate bed depression, but not all material needs
to be mobilized, just ample amounts to construct the redd. Spawning will not be successful if
adequate amounts of gravel-sized material cannot be mobilized. In salmonids, fish size is
directly proportional to maximum movable substrate size, and can be used to effectively
determine upper, species-specific size limit criteria for suitable spawning gravels. Kondolf
(2000) describes a method for determining appropriate spawning substrate size of a population
whereby the maximum movable substrate size for spawning female salmonids was defined as
10% of the average female’s length (Figure 27). We used sex and length data collected from
post-spawn coho salmon in the Scott River watershed (unpublished data provided by USFS) to
calculate the average female size, and used 10% of the average female’s length as the value to
define the maximum movable material size for this population. These data were then compared
against existing substrate conditions to determine habitat suitability indices. Specifically,
substrate D50 and D84 were used to evaluate the suitability of existing spawning habitat and
identify the potential for restoration in different mainstem and tributary reaches throughout the
watershed.
46
Figure 27. Median diameter (D50) of spawning gravel plotted against body length of a spawning salmonid.
Solid squares denote samples from redds; open triangles are ‘‘unspawned gravels,’’ which are potential
spawning gravels sampled from the undisturbed bed near redds (in Kondolf 2000 as modified from Kondolf
and Wolman 1993).
Gradient and substrate size provided a useful filter for differentiating potential coho spawning
reaches from low-potential sites throughout the Scott River Watershed (Figure 28). The model
did not perform well where we did not account for the ecological boundaries (see Cadenasso et
al. 2003) between various reaches. This can be observed, especially in the high-gradient
Tompkins and Canyon creeks, where we did not survey the creek deltas at their confluences with
the Scott River proper. South Fork Scott River, Reach 2 also indicated that D50 substrate was too
large for spawning (D50 = 99 mm). We assume that our sampling may not have accounted for
substrate segregation patterns that might provide pockets of appropriate spawning habitat.
47
Figure 28. Predicted potential spawning reaches using substrate size and estimated reach gradient. Coho
salmon redds identified during three years of surveys are overlaid. Black indicates no physical data collected.
48
Initial Screening of Sites
Using Chart 1, 14 sites were screened from the total data set meeting requirements for fish
passage, gradient, channel morphology, and substrate (Table 14)
Table 14. Study reaches that met initial screening criteria in Chart 1.
Reach ID
Stream
43
Shackleford Creek
40
Scott River
41
Scott River
12
French Creek
31
Patterson Creek
13
French Creek
9
Etna Creek
42
Scott River
4
Crater Creek
32
Patterson Creek
44
Shackleford Creek
35
S. Fork Scott River
18
Kidder Creek
19
Kidder Creek
Reach
1
3
4
1
1
2
1
5
1
2
2
2
1
2
Enhancement
Rank
1
2
3
4
5
6
7
8
9
10
11
12
13
14
Classify Enhancement Potential (Chart 2)
Once the coho spawning sites have been prioritized the enhancement potential of each site can be
further investigated. Chart 2 (Figure 29) continued to utilize the rigorous approach described
above to reveal the enhancement potential at each prioritized reach based on fine sediment and
pool ratios. This approach will provide for the greatest likelihood of success with potential
projects and is integrated into the social science prioritization developed by the SQRCD (see
below) to arrive at a refined list of sites with a high potential for successful enhancement.
49
Figure 29. Classification process of enhancement potential.
E. Fine sediment within the spawning substrate
For successful incubation, gravel must be sufficiently free of fine sediment so that the flow of
water through the gravel is adequate to bring dissolved oxygen (DO) to eggs and carry off
metabolic wastes (see discussions in Chevalier et al. 1984 and Groot and Margolis 1991) and fry
must be able to emerge from the substrate.
50
Figure 30. Percent fines in the Scott River watershed.
F. Pool Ratios within Appropriate Reaches
Other channel types of less that 4% slope represent important or potentially important spawning
and rearing areas for salmon but may lack some key roughness elements (e.g. large wood
material, boulders, etc.) and adequate pool frequency to support high juvenile and adult salmon
densities (Figure 31; Montgomery and Buffington 1997; Montgomery et al. 1999).
51
Coho
250
Redds/km
200
150
100
50
0
0
5
10
15
20
25
30
Pool spacing (CW/pool)
Figure 31. Regression model for coho spawning density as it relates to pool spacing (Montgomery et al. 1999).
Figure 32. Pool ratio in the Scott River watershed (Channel width/pool).
52
G. Potential enhancement alternatives for candidate reaches
According to Roni et al. (1999), the delineation of channel types based on slope allows
identification of potentially important and vulnerable habitats in the absence of complete or
accurate salmon distribution or habitat data. This process will also identify degraded stream
reaches, such as those lacking key roughness elements, and stream reaches with a high potential
for restoration as high-quality salmon habitat (Roni et al. 1999).
Classification of Impacted Habitat and Potential Enhancement
Table 15. Classification of impacted habitat and potential rehabilitation action.
Symptom
Insufficient
sediment
Description
Example
Potential
Rehabilitation Action
Sediment required for redd
Reach is too coarse for Gravel Augmentation
construction is lacking and limiting
slope and landscape
spawning in a reach that
position
otherwise meets spawning
requirements.
Insufficient
topographic
diversity
Morphologic units needed for
Coho lifecycle are lacking in a
reach that otherwise meets
morphologic requirements
Lack of pools, LWD,
riffles
Gravel
Augmentation;
Instream Structure
Insufficient
Sediment
Sorting
Overabundance of fine sediment
Reach is too fine for
slope and landscape
position
Instream Structure
Recommended Actions
We used the prioritization framework for Scott River coho salmon (Charts 1 and 2) to:

identify surveyed reaches that met the general requirements for coho spawning;

identify which, if any, of those identified in step 1 demonstrated physical properties that
were less than optimal for spawning and incubation;
We then followed the process (see Figure 26 and Figure 29) to identify the most beneficial
locations for spawning habitat restoration using the techniques of gravel augmentation and/or
structural enhancement.
Model Results
Ten (10) reaches within the Scott River watershed were identified as meeting the general
requirements for coho spawning habitat but demonstrating physical properties that were less than
53
optimal for spawning and incubation and having potential to benefit from gravel augmentation,
structural enhancement or a combination of the two.
South Fork Scott River, Reach 2
Candidate for Gravel and Structure Placement - Rank: High; High; High
Reach 2 of the South Fork Scott River was identified as a high priority candidate for gravel
augmentation and secondarily structural enhancement due its moderate potential for sediment
transport, above-threshold size (D50 = 99mm) surface substrate and lack of woody debris (0%
detected). Designation as a high priority site is due to two main factors: (1) the reach is
consistently opening during Coho spawning migration; and (2) has a preferred Coho stream
gradient (1.47%). Stream morphologies in the reach include riffle-pool (ratio 3.1) and step-pool
habitat considered moderately and highly preferred, respectively, spawning habitat for Coho
salmon (Montgomery et al. 1999). From 2001-2007, the Siskiyou RCD confirmed coho salmon
spawning activity in this reach. Under present conditions the model predicts embryo survival and
emergence of fry in the reach should exceed 75% due to the relatively low infiltration of fine
substrate in subsurface gravel.
Shackleford Creek Reach 2
Gravel and structural enhancement- Rank: Medium; High; High
Reach 2 of Shackleford Creek was identified as a moderate to high priority reach for gravel
augmentation because of its moderate probability of being open during the entire spawning
season, high quality gradient range for coho spawning selection, and because its D50 is slightly
larger than that identified by the model as optimum for Scott River coho. The model also
predicts high embryo survival with present levels of fine sediment. Therefore, the model
suggests that increasing the volume of gravel material within the size preferences for coho
salmon would increase spawning success. Coho spawning has been documented in this reach.
French Creek2
Structural enhancement; secondary: gravel augmentation- Rank: High; High; High
Reach 2 of French Creek was identified as a high priority reach for structural enhancement
because it has a high probability of being open during the spawning season, is within the high
quality range for gradient used by coho, falls well within D50 range for coho lengths within the
Scott River but has elevated fine sediment that the model predicts would reduce embryo survival
(72% survival). The reach has a low volume of woody material presently in the channel. Since
we predict relatively low transport of coho-sized spawning material, this reach could also benefit
from gravel augmentation to reduce the percentage of fine sediment relative to coarser particle
sizes. Coho spawning has been documented in this reach.
Scott River 4
54
Structural enhancement; secondary: gavel augmentation- Rank: High; High; High
Reach 4 of the Scott River was identified as high priority for structural enhancement because it
has a high possibility of being open during the spawning season, is within high quality gradient
range for coho spawning use and the existing D50 is well within the range predicted appropriate
by the coho length model. The embryo model predicts the reach is moderately impaired due to
fine sediment and the reach presently has little wood structure (none observed during survey).
Our modeling predicts relatively low transport rates for gravel of appropriate size for coho
spawning, suggesting gravel augmentation could also be used to reduce the percentage of fine
sediment relative to coarser particle sizes at the site.
Patterson Creek 2
Structural enhancement; secondary: gravel augmentation- Rank: Medium; High; High
Reach 2 of Patterson Creek was identified as a moderately high priority reach for structural
enhancement because it has a moderate possibility of being open during the spawning season but
is located within the high quality gradient range for coho spawning preference and the existing
D50 range is well within the range predicted appropriate for coho spawning. The embryo model
predicts the reach is moderately impaired due to fine sediment and the reach presently has little
wood structure (none observed during survey). The sediment transport model predicts moderate
transport rates for gravel appropriate for coho spawning suggesting possible benefits from gravel
augmentation to reduce the percentage of fine sediment relative to coarser particle sizes if
sufficient structure is added to the reach to maintain coarse material. Spawning coho have been
documented using this reach.
Scott River 3
Structural Enhancement; secondary: gravel augmentation- Rank: High; Medium; Medium
Reach 3 of the Scott River was identified as a high to moderate priority reach for structural
enhancement because it has a high probability of being open during the spawning season, is
located within the moderate quality gradient range for coho spawning preference and the existing
D50 range is well within the range predicted appropriate for coho spawning. The embryo model
predicts the reach is moderate to highly impaired due to fine sediment and the reach presently
has little wood structure (none observed during survey). The sediment transport model predicts
low transport rates for gravel appropriate for coho spawning suggesting possible benefits from
gravel augmentation to overwhelm fine sediment. We found no documentation of coho
spawning use in this reach over the past 15 years.
Etna Creek, Reach 1
Structural enhancement; secondary: gravel augmentation- Rank: Medium; Medium; High
Reach 1 of Etna Creek was identified as a moderate priority candidate for structural enhancement
due to a moderate probability of being open for the entire spawning season, moderate slope
55
preference by spawning coho salmon and its the existing D50 falling within optimum for
spawning coho salmon. Etna Reach 1 is slightly impaired due to elevated fines which could
benefit from structural enhancement. Because of its relatively low ranking for coho spawning
material mobilization, this reach could also benefit from gravel augmentation to reduce the
percentage of fine sediment relative to coarser particle sizes.
Kidder Creek2
Structural enhancement; secondary: gravel augmentation- Rank: Medium; Medium; High
Reach 2 of Kidder Creek was identified as a moderate to high priority reach for structural
enhancement because it has a moderate probability of being open during the spawning season, is
located within the moderate quality gradient range for coho spawning preference and the existing
D50 range is well within the range predicted appropriate for coho spawning. The embryo model
predicts the reach is moderate to highly impaired due to fine sediment and the reach presently
has little wood structure (none observed during survey). The sediment transport model predicts
little to no sediment transport into this reach and so Reach 2 of Kidder Creek may also be
appropriate for gravel augmentation. Coho spawning has been documented in this reach.
Patterson Creek 1
Structural enhancement; secondary: gravel augmentation- Rank: Medium; Medium; High
Reach 1 of Patterson Creek was identified as a moderate to high priority reach for structural
enhancement because it has a moderate probability of being open during the spawning season, is
located within the moderate quality gradient range for coho spawning preference and the existing
D50 range is well within the range predicted appropriate for coho spawning. The embryo model
predicts the reach is moderately impaired due to fine sediment and the reach presently has little
wood structure (less than 0.5% coverage). The sediment transport model predicts low transport
rates for gravel appropriate for coho spawning relative to other sites suggesting possible benefits
from gravel augmentation to reduce the percentage of fine sediment relative to coarser particle
sizes. Coho spawning has been documented in this reach.
Kidder Creek 1
Structural enhancement; secondary: gravel augmentation- Rank: Medium; Medium; Medium
Reach 1 of Kidder Creek was identified as a moderate priority reach for structural enhancement
because it has a moderate probability of being open during the spawning season, is located
within the moderate quality gradient range for coho spawning preference and the existing D50
range is well within the range predicted appropriate for coho spawning. The embryo model
predicts the reach is moderate to highly impaired due to fine sediment. The reach habitat is plain
bed with no observed pools within the study reach and no wood structure observed during the
survey. Structural enhancement would be a priority for this reach. The sediment transport
model predicts little to no sediment transport within this reach and so it may also be appropriate
for gravel augmentation. Coho spawning has been documented in this reach.
56
SPAWNING GRAVEL ENHANCEMENT PLAN AND RECOMMENDED
ACTIONS
Potential Enhancement Tools
This section provides descriptions of various techniques that can be applied to each phase of the
rehabilitation/enhancement process, depending on site-specific conditions. The techniques,
including possible applications, considerations and costs, are described below. In many
situations, more than one technique can be used. Because a variety of site conditions will occur
and are specific to each potential enhancement site, the conditions require evaluation to identify
the most appropriate treatments to be used. Examples of site conditions requiring evaluation
include existing and historical channel morphology, riparian vegetation community, salmonid
spawning use, adjacent land use, and erosion potential.
Other elements to be considered are site access, budget and material availability and an overall
cost/benefit analysis. Many of these issues are not particularly suitable for a scientific
assessment. We believe these are more appropriately assessed through a watershed stewardship
program or stakeholder group to prioritize projects by costs, community interests and
accessibility to potential sites. Potential prioritization scheme is discussed below and Table 16
summarizes the potential techniques.
Gravel for spawning habitat rehabilitation is typically purchased from floodplain quarries or inchannel mining sources (Kondolf 2000). Ideally, a source exists within the basin, but often
gravel may only be available from other basins posing ethical questions pertaining to enhancing
one drainage at the expense of another. In California, the cost for each metric ton of concretegrade aggregate can range from USD $7.00 – $20.00 at the mine, plus an additional USD $0.06 –
$0.10 km-1 for site transportation (Merz et al. 2006). Cost for in-basin river gravel including
triple-washing and transport was USD $22.90 m-3 total. The cost for gravel placement
equipment and labor was an additional USD $0.47 m-3 (2% of purchase and transport).
Depending on fuel costs and site location, costs can be as high as $45.00 m-3 for placement
completion (CDFG, unpublished data; USBR, unpublished data), and can be further influenced
by the housing market, state and federal road projects, and even the global economy. As gravel
is sold by weight, some volumetric loss may be due to over estimates in mass to volume
conversions and loss at storage sites (Merz et al. 2006).
57
Table 16. A summary of salmonid spawning habitat enhancement/ augmentation techniques.
Method
Success/conditions for use
Timing
Costs
Special consideations
Gravel Injection
Used where flows are high enough to
mobilize material; Bank or drop location
with easy access to river channel upstream
of where gravel is needed; typically used
where a reservoir or other structure limits
coarse sediment passage or to mitigate for
past or present mining efforts
Material typically can be
placed at any time but
usually done to coincide
with high flow events; may
take several months to get
appropriate gravel mix
made
Often one of the cheapest methods;
expense primarily associated with fuel
costs for gravel delivery; Gravel costs
increase with specialization of size
classes. At present $15-20 per ton plus
$0.16- 0.20 per mile transport; permitting
may be several thousand dollars.
It is often best to find "within basin" material to
avoid impacting other watersheds and increase
use by "local" fish; If there is no quarry available,
you may want to mine your own material if
available on site; especially mining tailings; Any
material that must be transported from one
location to another via public roads will require
SMARA permitting; you may need to wash
gravel which also requires special
considerations with water rights or water quality
restrictions; this technique may take years to
demonstrate "success"
Spawning Bed Enhancement
Locations where flows are either too low to
mobilize, clean and segregate coarse bed
sediment or regulation has limited the
source of coarse sediment. In either case
this option is typically chosen when
immediate habitat availability is needed.
Typically must avoid timing
for sensitive species,
especially aquatic; This
often leaves late summer
to early autumn period
only; may take several
months to get appropriate
gravel mix made
Technique more expensive than
Injection; Typically requires engineering
designs. Strategically placed, washed
-1
material may costs $25 ton but as much
-3
-1
as $45 m (33 ton ); permitting may be
several thousand dollars.
Requires in-stream work with heavy equipment;
see notes above for gravel sources etc; Permits
may take 6 - 18 months; If fish are available,
may be used immediately; May require
maintenance if natural coarse sediment is
limited
Hydraulic structure placement
Typically used where channelization, or
flashy flows mobilize coarse materials; Can
also be used in limited situations where
high fine volume can be segregated from
coarse bed material; Also when woody
vegetation and debris have been reduced
or removed from the system
If heavy equipment used in
stream or bank, must avoid
timing for sensitive
species, especially aquatic;
This often leaves late
summer to early autumn
period only;
This is perhaps the most expensive of
the projects for size; Individual structural
projects may cost as little as $1,500 for
small streams to over $100k for large,
engineered strcutures on mainstems.
Materail such as trees that are available
on site may significantly reduce costs;
local timiber harvests may be willing to
collaborate as mitigiation for their work
Requires in-stream work with heavy equipment
in most cases. Rarely can be done by hand
crew or crane. Permits may take 6-18 months;
Permits may take 6 - 18 months; Sediment
scour, deposition or segregation will require at
least 1 high flow event to see results
58
Gravel Injection
Gravel Injection (also known as gravel replenishment) seeks to replenish some portion of a
regulated river’s sediment budget deficit with imported sediment (Figure 33). This is typically
achieved by dumping clean spawning gravels into piles along the edges of a stream at locations
upstream of degraded spawning habitat reaches (usually just downstream of a dam). It is
assumed that augmented gravels will be entrained during high flows with the competence to
transport them downstream. Designs are rarely necessary for gravel augmentation, but a
sediment budget and a monitoring program to enable adaptive management are appropriate.
Figure 33. Gravel injection below Englebright Dam, Yuba River, California. Photo courtesy of U.S. Army
Corp of Engineers.
Spawning Bed Enhancement
Spawning bed enhancement includes direct modifications to the bed (e.g. riffle construction, bed
ripping and riffle cleansing) (Figure 34). Spawning bed enhancement that involves placement of
gravel differs from gravel augmentation in that the augmented gravels are placed as specific bed
features (typically riffles or bars), potentially providing immediate spawning habitat. Spawning
bed enhancement can be used to improve the fluvial complexity of channels detrimentally
simplified for flood control or mining purposes. Placed gravels are intended to decrease local
depth and increase velocity to better match observed spawning preferences. Although bed
enhancement may quickly provide usable spawning habitat, limited project life spans may result
without adequate consideration of geomorphic processes.
59
Figure 34. Strategic gravel placement on the lower American River, California.
Hydraulic Structure Placement
Physical Function of Structures
All structures placed in a channel have the potential to affect channel hydraulics, sediment scour
and deposition patterns, and wood and sediment transport. According to Washington Department
of Fish and Wildlife (WDFW 2002), the degree to which these effects achieve the desired results
or place nearby habitat, infrastructure, property, and public safety at risk depends on a number of
important variables that affect the way in which a structure functions in the stream. The
following parameters should be considered in structure design:

Channel constriction caused by the structure

Location of the structure within channel cross-section and its height relative to the flow depth

Structure spacing

Structure configuration and position in the channel

Sediment supply and substrate composition

Channel confinement

Hydrology

Time
The effects of these variables vary along a continuum, ranging from slight changes in channel or
floodplain, to catastrophic channel aggradation, incision, or avulsion. Where a given project
should be on this continuum depends on the project goals, which must be clearly identified from
the outset. There are always potential unintended consequences of any structure placement. The
designer should be aware of these consequences and realize that forces in streams act in ways
that are beyond our control.
60
Placement of Structures
The most common type of Spawning Habitat Rehabilitation (SHR) is hydraulic structure
placement (often called habitat enhancement or instream structures). Physical structures (e.g.
large wood material, boulder clusters, v-dams, half-log covers, deflectors) are placed in the
channel to alter hydrodynamics in such a way that spawning gravels are deposited in the vicinity
of the structures. The technique relies on an adequate upstream supply of appropriately-sized
gravel and an active bedload transport regime to deliver it. Such structures may also be intended
to provide refugia, cover and add habitat heterogeneity. In other instances, hydraulic structures
are intended to promote pool scour. The implementation of hydraulic structure placement is
typically prescriptive and often lacks adequate process considerations (Wheaton et al. 2004).
The term “structure” (in the context of spawning habitat) refers to any intentionally placed object
in the stream to (a) obstruct streamflow and force it to move around the structure or (b) provide
cover to fish in the form of a visual or solar barrier. Because flow must accelerate as it moves
around an object, its ability to carry sediment increases. As it passes the object, velocities
typically decrease and water loses its ability to carry sediment. Structure, such as logs and snags,
has been shown to cause local scour (Beschta, 1983; Lisle 1986; Bilby and Ward 1991), and to
increase pool frequency (Hogan, 1987; Robison and Beschta 1990; Montgomery et al. 1995) and
hydraulic roughness (Lienkaemper and Swanson 1987; Montgomery and Buffington 1993). This
redirection, concentration, or expansion of flow influences the form, structure, hydraulics, and
consequently, the function of the stream. Studies indicate that LWM creates scour pools that
provide rearing and resting habitat for salmonids and other fish and collects sediment that is used
by spawning salmon (Harmon et al. 1986; Lisle 1986; Merz 2001). However, instream structures
are prone to having unintended consequences; caution must be exercised when using this
approach.
Structures encompass a broad range of objects, consisting of differing materials, functions,
longevity, and scale. The most common structural enhancement materials are logs (a.k.a. Large
Woody Debris or Material) and boulders. However porous weirs and drop structures are often
used in the Pacific Northwest (Table 17). The size and quality of the material used can have
major ramifications for project success and support from local community and resource agencies.
Logs missing root wads or canopy may not function as well hydraulically or ecologically
(Rosenfeld and Huato 2003). Broken rock or riprap may provide adequate results for habitat
complexity but are aesthetically unpleasing.
61
Table 17. Primary functions of instream structures in habitat applications. Source: Taken from Washington
Department of Fish and Wildlife (2004).
Large
Wood &
Log Jams
Boulder
clusters
Porous
Weirs
Drop
Structures
Create bed and bank scour
YES
YES
YES
YES
Sort sediment
YES
YES
YES
YES
Create backwater
YES
YES
YES
YES
Stabilize or raise streambed
YES
NO
YES
YES
Alter stream grade
YES
NO
YES
YES
Provide cover, resting and high flow refuge
YES
YES
YES
NO
Armor streambanks
YES
NO
NO
NO
Improve wildlife habitat
YES
YES
NO
NO
Redirect flow
YES
YES
YES
YES
Trap material
YES
YES
NO
NO
Provide fish passage
YES
NO
NO
YES
Application
Placement of instream structures is commonly done to improve instream fish habitat (Figure 35).
These structures are typically intended to serve as analogs to otherwise naturally-occurring
features (WDFW 2004). Certain benefits associated with instream structures (such as cover,
shelter from fast moving current, or creation of velocity gradients) are available to fish and
wildlife immediately following their installation. However, other benefits (such as scour,
deposition, or sorting of bed material) may require several high flow events before they are
realized. Instream structure installation can be successful. However, there is a tendency when
using this approach to focus on the symptoms of habitat degradation rather than the cause (Roper
et al. 1997), to implement without full understanding of resource needs (Beechie and Bolton
1999), and to provide benefits for a specific target fish species, sometimes at the expense of other
fish and wildlife (Frissell and Ralph 1998). As a result, benefits may be temporary without
maintenance and repeat application, they may be limited in scope, or they may never be achieved
if the treatment does not address the factors that limit ecosystem productivity and recovery. In
addition, incorrectly designed or constructed structures are prone to failure and causing further
ecosystem degradation (Beschta et al. 1992). It should be noted that instream structures are
temporary fixes to larger systemic watershed issues (Roni et al. 2002). Moreover, instream
structures have a limited lifespan and may lose functionality over time (Thompson 2006).
62
Figure 35. Fall-run Chinook salmon spawning adjacent to large boulders placed in lower Mokelumne River,
CA. Log jam placed adjacent to spawning gravel to provide heterogeneity.
Roni et al. (2002) found that the success of common instream structure projects was quite
variable and depended upon the species studied and project design. Instream structures are most
effective at restoring or rehabilitating ecosystems when they address the principal cause of
ecosystem degradation or when they are used to provide immediate improvement of habitat
condition in conjunction with other techniques that address the root cause of the problem. They
can also be used to enhance habitat when the materials and processes necessary for the natural
occurrence of desirable habitat features and conditions are absent and cannot be restored given
current constraints or be used until the system is able to recover and function on its own (e.g.
coarse wood input from a functional riparian zone).
Considering the risk of project failure and unintended consequences, structure installation and
other instream rehabilitation or enhancement work should only be conducted with adequate site,
reach, and watershed assessment to determine the nature and extent of problems in the
watershed, determine the nature and extent of the cause(s) of those problems, and to establish
realistic restoration goals, objectives, and priorities.
The Spawning Habitat Integrated Rehabilitation Approach
Wheaton et al. (2003) developed Spawning Habitat Integrated Rehabilitation Approach (SHIRA)
for use on salmonid spawning habitat rehabilitation projects in regulated rivers. The approach is
driven by a mix of field data, conceptual models, and numerical algorithms to provide predictive
and explanatory insight into the design and planning process. At the heart of SHIRA is a
conceptual spawning model that explicitly identifies the assumptions behind the approach
(Figure 36). Although, this approach was developed specifically for spawning habitat restoration,
many of its components are directly transferable to other forms of river restoration. There are
other methods set forth in the literature (see Roni et al. 2002 as an example).
63
Figure 36. Conceptual spawning habitat model. The arrows indicate influences, the circles represent
processes and characteristics, and the boxes are the results.
A combination of hydrogeomorphic processes spanning a range of scales combine to create
physical habitat. Physical habitat is chosen by females for redd construction based on the
ecologic functions provided by physical habitat and ecologic factors including habitat
heterogeneity, run size, timing, social factors and physiology. The survival of alevins and
ultimate emergence of fry is then primarily controlled by the substrate and local flow conditions
during the incubation period (taken from Wheaton et al. 2004) (Figure 37).
64
Figure 37. The SHIRA flowchart. The two primary components are phases and modes. Projects progress
sequentially through specific project phases, ranging from the initial problem identification to long-term
monitoring and adaptive management. During each of seven phases, four primary modes are used to collect
and analyze data on which informed decisions can be based (from Wheaton et al. 2004).
Before implementing a process such as SHIRA, we also recommend the following steps:
1. Identify stakeholders and interests
2. Identify project constraints (see below)
3. Define project goals and objectives
4. Evaluate the risks to the environment, infrastructure, property, and public
safety that are associated with both project installation and failure
Additional Considerations for Prioritization of Enhancement Projects
Within this endeavor, we have developed a means to measure and prioritize the relative quantity
and quality of salmonid spawning habitat (emphasizing coho salmon) within accessible areas of
the Scott River Watershed. This process can be used to identify the most critical habitats for
enhancement but also identify key areas presently available to target species. For reaches that
65
appropriately demonstrate the need for enhancement, the users of this program will need to also
prioritize potential projects sites by cost, equipment accessibility, landowner willingness, area
size, and goals for the Scott River Watershed in relationship to salmonid ecology and local
community needs and concerns. These are issues are better addressed by stakeholder consensus
rather than a scientific evaluation. Table 18 contains subjects that we believe are some of the
key parameters that must be evaluated to prioritize restoration sites along with a mock-up of a
potential scoring system to help prioritize sites. These parameters are provided as a starting
point for dialog between watershed stakeholders about projects to benefit Scott River salmonid
resources but that also meet the social and financial concerns and needs of the Scott River
Watershed community.
Estimating Costs
The cost of LWM projects varies with the complexity of the design, site accessibility, flow
conditions, and cost of LWM. Cederholm et al. (1997) estimated costs of LWM projects to vary
by an order of magnitude ($12.90 vs. $164.50 per meter of channel length) due to differences in
design complexity alone. There were some economic decisions that had to be made for the
restoration of Elk Creek in Oregon because the equipment to perform the stream restoration had
to be rented. Track-mounted excavators were used to install logs at a cost of $90-$100 per hour.
The total Elk Creek restoration project cost $46,200 (including equipment and labor) in which
approximately 2 km of the Nustucca River and Elk Creek were treated with 119 log structures
(House et al. 1990). On another project, the restoration of Testament Creek in Oregon, a timber
sale contract was modified at a cost of $50 per tree bole to pay loggers to place nonmerchantable wood material into the stream. A medium sized caterpillar tractor was also rented
at approximately $50-$60 per hour to assist in placing the wood structure into the stream (House
et al. 1989).
Contacting county and state road repair crews before winter storms is a good way to develop a
“free” source of LWM. However, the material must then be secured and transported to the
project location. Purchasing logs can be quite expensive (Table 19). Other sources include
downed trees in parks and woody material collection in local reservoirs.
66
Table 18. Stewardship prioritization in the Scott River watershed.
Score
3
2
2
4
Subject and evaluation
Species Benefits
Project will benefit coho salmon spawning
Project will benefit Chinook salmon spawning
Project will benefit steelhead spawning
Project will benefit coho and at least one other salmonid spawning
3
2
1
Project longevity
Project will have significant long-term benefits for salmon spawning (>5 yr)
Project will have moderate long-term benefits for salmon spawning (3-5 yr)
Project will have relatively short-term benefits for salmon spawning (1-2 yr)
3
2
1
Engineering feasibility
Would require limited engineering; liability low
Would require moderate engineering; potential for some liability
Would require expensive and complex engineering; High liability
4
3
2
1
Overall project size
>1 acre of channel improvement
1/2 - 1 acre of channel improvement
1/4 - 1/2 acre of channel improvement
<1/4 acre of channel improvement
3
2
1
0
-1
Cost
<$50k
$50 - 100k
$101 - 200k
$201 - 500k
>$500k
Scale of project improvement - "Bang for the Buck"
cost divided by acreage
3
0
Landowner access- willing private or public owner
Yes
No
3
2
1
Equipment accessibility
Easy access - Pre-existing roads; low slope; all equipment accessible with little or no modification to existing conditions
Moderate - some difficulty in getting equipment to the site
Difficult- may need to build roads or other access; slope may restrict access to most equipment
3
2
1
Environmental Response
Short-term (immediate) - Should see immediate, measurable response to target organsim(s) from project
Moderate response - May see limited response within 1-3 years after implementation
Long-term - May take several years to see any measureable
3
2
1
Probability of success
High probability of success
Medium probability of success
Low or unknown probability of success
3
2
1
3
2
1
Educational benefits
Project ability to provide important information for future restoration and management is high long-term monitoring has occurred at site; funding available for continued tracking
Project ability to provide important information for future restoration and management is moderate some pre-existing data present - possible monitoring to continue
Project ability to provide important information for future restoration and management is low no pre-existing monitoring or data exists; little or no potential for post-project monitoring
Collaboration potential
Project has pre-existing funds available; Can coordinate with other activities
Project has limited pre-existing funds available; Some potential to coordinate with other projects
Project has no pre-existing funds; no potential to coordinate with other projects
67
Recent equipment estimates for loader and skidders in California is $100 – 250 per hour per
piece of equipment. For more inaccessible areas, helicopter rental can be $1000 – 8000 per hour.
River-run boulders have recently cost $40 -80 per ton for transport to enhancement locations
(Merz, unpublished data).
Table 19. Approximate cost (2010 year dollars) for common varieties of timber in Siskiyou County. Assume USD
$0.06 – $0.10 km-1 for transportation costs from harvest location to enhancement site per log. Logs containing
rootwads and/or canopy will be much more expensive.
Ponderosa Pine
Volume/16 ft Log
>300
150-300
<150
Western Siskiyou
Green Timber Salvage Timber
$170
$130
$90
$70
$10
$10
Eastern Siskiyou
Green Timber Salvage Timber
$250
$190
$190
$140
$100
$60
Max.
$250
$190
$100
Overall
Min.
$130
$70
$10
Avg.
$185
$123
$45
Hemlock/Fir
N/A
$20
$15
$100
$50
$100
$15
$46
Douglas Fir
>300
150-300
<150
$150
$100
$80
$110
$80
$60
$190
$170
$120
$140
$130
$90
$190
$170
$120
$110
$80
$60
$148
$120
$88
N/A
$280
$210
$370
$280
$370
$210
$285
>125
$400
$300
N/A
N/A
≤125
$300
$220
N/A
N/A
*All values are from the California State Board of Equalization (January 1, 2010 through June 30, 2010)
**All values are based on use of conventional logging systems
***Values are in Dollars/MBF
****Volumes are in MBF (thousand board feet)
$400
$300
$300
$220
$350
$260
Incense Cedar
Port-Orford Cedar
Gravel Sources for the Scott River
If gravel enhancement is a chosen management decision in the Scott River drainage, reliable,
quality material will be needed. The Scott River Watershed was heavily mined for precious
metals (primarily gold). Gravel mining has occurred throughout the past 50-80 years and
continues on a smaller-scale today.
Gravel Purchase
We surveyed records of gravel mining sources for the state of California (CALTRANS records).
We found six businesses based out of the Scott River Watershed (Etna, Callahan, Fort Jones) that
commercially sell gravels. Two gravel sources already provide screened material for
enhancement (see Figure 38).
68
Figure 38. Potential gravel sources near the Scott River; Dredger tailings.
Reclamation
Gold dredgers deposited processed materials in long rows on the floodplain of many rivers
throughout California. During the period from 1934 to about 1950, large gold dredges operated
on the upper Scott River and Wildcat Creek. The largest dredge excavated to a depth of 50-60
feet below water line and processed millions of cubic yards of soil and gravel (Sommarstrom et
al. 1990). These tailings consist of fine sand and gravel overlain by cobbles and boulders.
Tailings currently cover approximately 372 acres of floodplain in vicinity of Callahan (Figure
30). We estimated tailing elevations of 10 to 50 feet during habitat surveys. This suggests that a
conservative estimate of the volume of these tailings to be approximately 6.1 million yd3 (this
should be evaluated more fully). This offers an opportunity to reclaim these materials for gravel
enhancement and restoration of riparian floodplain. Such work can also have positive effects on
ground water recharge. Similar work is being performed on the Trinity River and Central Valley
rivers such as the American and Merced. Permitting (per Surface Mining and Reclamation Act
requirements), archeological resources and remnant hazards (i.e., mercury) are issues that must
be addressed.
Permits and Approvals for Spawning Habitat Enhancement
The following permits/authorizations are/may be required to implement a project as of August 2010:
Section 404 of the Clean Water Act and Section 10 of the Rivers and Harbors Act
The U.S. Army Corps of Engineers is authorized to issue permits for discharges of
dredged or fill material into waters of the United States. Gravel augmentation is
69
considered fill material. Applications will be made for a Nationwide Permit 27 for the
restoration of wetland and riverine habitats.
NO FEE; WATER QUALITY CERTIFICATION REQUIRED
Section 401 of the Clean Water Act
State water quality standards cannot be violated by the discharge of fill or dredged
material into waters of the U.S. The State Water Quality Control Board, through the
Central Valley Regional Water Quality Control Board, is responsible for issuing water
quality certifications, or waivers thereof, pursuant to Section 401 of the Clean Water Act.
$640 FEE FOR RESTORATION PROJECTS; CEQA COMPLIANCE REQUIRED
Federal Endangered Species Act (ESA)
Section 7 of the ESA requires all federal agencies to consult with the USFWS and
National Marine Fisheries Service (NOAA Fisheries) to ensure that their actions do not
jeopardize the continued existence of endangered or threatened species or result in the
destruction or modification of the critical habitat of these species. The Secretary of
Commerce, acting through NOAA Fisheries, is involved with projects that may affect
marine or anadromous fish species listed under the Endangered Species Act (ESA). All
other species listed under the ESA are under USFWS jurisdiction.
NO FEE
National Environmental Policy Act (NEPA)
National Environmental Policy Act (42 USC 4321, 40 CFR 1500.1) applies to any action
that requires permits, entitlements, or funding from a federal agency; is jointly
undertaken with a federal agency; or is proposed on federal land. The Act requires every
federal agency to disclose the environmental effects of its actions for public review
purposes and for assisting the federal agency in assessing alternatives to and the
consequences of the proposed action. An Environmental Assessment (EA) is typically
prepared to determine whether the project may have a significant environmental effect. If
the project would not have a significant effect or if mitigation incorporated into the
project description would reduce the project’s effect to a less-than-significant level, a
Finding of No Significant Impact (FONSI) is prepared along with an EA; otherwise, an
Environmental Impact Statement (EIS) is required. The EIS must consider, disclose, and
discuss all major points of view on the environmental impacts of a proposed project and
alternatives. The draft EIS must be circulated for public and agency review and
comment. The U.S. Environmental Protection Agency (EPA) is authorized to review and
comment on the environmental impact of matters subject to NEPA. After comments are
received and reviewed, the final EIS is prepared and circulated and the lead agency issues
a Record of Decision, which certifies compliance with NEPA and specifies mitigation
requirements and commitments.
California Environmental Quality Act (CEQA)
In addition to complying with NEPA, the action must be in compliance with CEQA.
Compliance with CEQA is required for implementation of restoration actions when:
 A California state, regional, or local agency approval or other discretionary
action is required; or,
 A state or local agency is solely or partially a project sponsor.
An Initial Study (IS) must be developed which includes the CEQA checklist for
environmental impacts. A combined document (EA/IS) can be developed when the
project must meet both NEPA and CEQA requirements. The CEQA process is similar to
that required by NEPA, and requires state, regional, and local agencies to assess the
environmental effects of proposed projects and to circulate these assessments to other
70
agencies and the public for comment before making decisions on the proposed projects.
The Act applies to an action that is directly undertaken by a California public agency; is
supported in whole or part through California public agency contracts, grants, subsidies,
loans, or other assistance from a public agency; or, involves California public agency
issuance of a permit, lease, license, certificate, or other entitlement for use by a public
agency.
NEED TO DETERMINE STATE LEAD AGENCY; REVIEW DOCUMENT WITH
LEAD AGENCY; SEND UP TO 16 COPIES FOR DISTRIBUTION FROM THE
STATE CLEARINGHOUSE; NO FEE
California Endangered Species Act (CESA), California Fish and Game Code 2081, 2090
The California Endangered Species Act (CESA) allows CDFG the ability to authorize, by
means of an incidental take permit, incidental take of state-listed threatened, endangered
or candidate species if certain conditions are met. For CDFG projects, routine internal
coordination occurs whenever CDFG proposes a project, which may impact a state-listed
species of plant or animal. The CDFG strives to ensure that no threatened or endangered
species would be adversely affected by their projects, even for projects otherwise exempt
from the California Environmental Quality Act (CEQA). When CDFG proposes to
undertake a project that has the potential for take of a state-listed species, if the project is
part of the management of that species, i.e., for the protection, propagation, or
enhancement of the species and its habitat, CDFG is not required to get a CESA
Incidental Take Permit per California Code of Regulations, Title 14, Section 783.1.
However, CDFG is still required to complete its obligations under CEQA and prepare a
Negative Declaration or an EIR, as appropriate, for the proposed project.
The Fish and Wildlife Coordination Act
The Fish and Wildlife Coordination Act requires federal agencies to consult with
USFWS, NOAA Fisheries, and state fish and wildlife resource agencies before
undertaking or approving water projects that control or modify surface water. The AFRP
will work to ensure the proposed project’s compliance with the Fish and Wildlife
Coordination Act.
The Essential Fish Habitat (EFH) provisions of the Magnuson-Stevens Fishery
Conservation and Management Act of 1996
The EFH provisions require federal agencies to consult with NOAA Fisheries on project
actions that may adversely affect the habitats of the west coast salmon fisheries and other
fisheries managed in federal waters.
NO SPECIFIC ACTIONS; ADDRESSED IN SECTION 7
Fish and Game Code Section 1600 et. seq., Streambed Alteration Agreement
California Department of Fish and Game has regulatory authority with regard to activities
occurring in streams and/or lakes that could adversely affect any fish or wildlife resource,
pursuant to Fish and Game Code Section 1600 et seq. Authorization is required for
proposed projects prior to any activities that could substantially divert, obstruct, result in
deposition of any debris or waste, or change the natural flow of the river, stream, or lake,
or use material from a stream or lake.
FEE DETERMINED BY COST OF PROJECT; CEQA COMPLIANCE REQUIRED
Central Valley Flood Protection Board (CVFPB) Encroachment Permit
The CVFPB issues permits to maintain the integrity and safety of flood control project
levees and floodways that were constructed according to flood control plans adopted by
the Board of the State Legislature.
71
NO FEE; CEQA COMPLIANCE REQUIRED
State Lands Commission Land Use Lease
The State Lands Commission has jurisdiction and management control over those public
lands received by the state upon its admission to the United States in 1850 that generally
include all ungranted tidelands and submerged lands and beds of navigable rivers,
streams, lakes, bays estuaries, inlets, and straits.
FEE $3,025 ($3,000 staff time; $25 filing fee); COUNTY APPROVAL NEEDED FOR
APPLICATION
County Approval
There may be permits specific to the county the project occurs in that need to be
acquired. At the minimum, it is necessary to obtain a letter of approval from the county to
include with the application for the State Lands Commission Land Use Lease.
Local Approvals
If project occurs within the city limits, it may be necessary to check with the local city
council about project activities and obtain any local permissions or permits.
Adjacent Landowner Approval
Adjacent landowner approval may be required by the city or county for project actions to
occur. The State Lands Commission Land Use Lease also requests a letter of project
support from the adjacent landowners.
National Historic Preservation Act, Section 106
Projects must coordinate with the State Historic Preservation Office and the Advisory
Council on Historic Preservation regarding the effects that a project may have on
properties listed, or eligible for listing, on the National Register of Historic Places.
Section 106 also requires federal agencies to evaluate the effects of federal undertakings
on historical, archaeological, and cultural resources. The AFRP will work to ensure the
proposed project has compliance with Section 106 of the National Historic Preservation
Act.
NO FEE
Local Air Pollution Control District
Certain districts require that all portable equipment registrations be obtained for all
project equipment.
Floodplain Management - Executive Order 11988
Executive Order 11988 requires that all federal agencies take action to reduce the risk of
flood loss, to restore and preserve the natural and beneficial values served by floodplains,
and to minimize the impact of floods on human safety, health, and welfare.
Protection of Wetlands - Executive Order 11990
Executive Order 11990 requires federal agencies to follow avoidance, mitigation, and
preservation procedures with public input before proposing new construction of wetlands.
Environmental Justice in Minority and Low-income Populations-Executive Order 13007Executive Order 12898
72
Executive Order 12898 requires federal agencies to identify and address
disproportionately high and adverse human health and environmental effects of federal
programs, policies, and activities on minority and low-income populations.
Indian Trust Assets, Indian Sacred Sites on Federal Land-Executive Order 13007, and
American Indian Religious Freedom Act of 1978
These laws are designed to protect Indian Trust Assets, accommodate access and
ceremonial use of Indian sacred sites by Indian religious practitioners and avoid
adversely affecting the physical integrity of such sacred sites, and protect and preserve
the observance of traditional Native American religions, respectively.
CONCLUSIONS AND MANAGEMENT IMPLICATIONS
.
Answers to Priority Study Questions
Is the rate of coarse sediment delivered to spawning reaches in the Scott River (upper river and
canyon reach) and in its tributaries limiting spawning habitat availability of current and
projected population targets?
Transport capacity and sediment supply index results show that downstream trends in gravel are
generally consistent with the scientific literature (for discussion see Constantine et al 2003).
Other than the two anthropogenic barriers on Etna Creek and the mainstem Scott River, gravel
transport is unimpeded. Pebble count data and survey data indicate that suitable gravels sizes are
found in conjunction with slopes also suitable for spawning. These observations suggest that the
amount of coarse sediment and its rate of delivery are not limiting spawning habitat availability
in the Scott River Watershed.
Is the quality of the existing spawning gravel impaired by excessive fine sediment?
The monitoring program identified existing levels of fine sediment that indicate impaired
salmonid spawning areas of the Scott River Watershed. This is not new information; other
studies within the watershed have documented fine sediment issues (Sommarstrom et al 1989;
Quigley 2008). However, the Plan’s embryo survival modeling exercise equated fine sediment
levels to salmon embryo survival throughout reaches of the watershed accessible during this
survey and demonstrated a wide range of habitat quality, including very high and extremely low
survival estimates. This method will allow for monitoring how well watershed management,
including enhancement and recovery, will influence the quality of habitat for salmonid embryo
incubation and survival.
Identification of Physical Processes Relevant to Spawning and Incubation Success
Salmon producing streams generally need three basic ingredients: water, sediment, and coarse
woody material. When supplied at rates, magnitudes and quality that are complementary to the
complex life history needs of salmonids, physical habitat is generally present and of suitable
quality to meet spawning, incubation and emergence requirements. We integrated topographic
data, air photos and site reconnaissance information to help establish linkages between historic
and current land use, intrinsic landscape processes and salmonid habitat to determine what
73
physical processes, specific to the Scott River watershed, are relevant to spawning and
incubation success. In the Scott River watershed a legacy of historic impacts still bares its mark
on channel morphology and riparian plant communities. These historic effects comingle with
modern impacts, affecting present day physical habitat quantity and quality.
Channel morphology is the expression of a complex suite of physical processes operating over a
variety of temporal and spatial scales. Our study shows that channel morphology in many
locations has been detrimentally impacted from historic and modern disturbances. The most
basic signature of this disturbance is a uniform channel geometry with poorly sorted (e.g.
unorganized variation in surface sediment size and/or orientation) sediments. It is known in
fluvial geomorphology that variations in channel width and depth co-vary. In instances where
we noted inadequate pools, the channel was typically confined and had very little variation in
channel width. Moreover, in streams where sediment sorting was poor we noted that there was a
uniform channel width and/or a lack of structural elements that create diverse hydraulic and
sediment sorting patterns.
Forced pool habitat associated with woody material is considered one of the highest-used
spawning habitats for coho salmon (Buffington et al. 2004). Our study also revealed that the
occurrence of LWM (e.g. logs, rootwads, snags) in sampled streams is much less than what the
scientific literature suggests is needed for salmonids. Researchers sometimes quantify the
amount of LWM in streams by using the number of pieces per 100 m that are large enough to
influence the channel characteristics (Stillwater Sciences 1997). House and Boehne (1986)
estimated that, in a relatively undisturbed section of a small stream in Oregon, there were 18
pieces of LWM per 100 m large enough to influence the channel. Sedell et al. (1982; 1984)
found that five (1982 study) and four (1984 study) pieces of LWM per 100 m influenced the
stream channel by creating pool habitat in undisturbed channels of the South Fork Hoh River,
Washington. Bilby and Ward (1989) surveyed characteristics of LWM in western Washington
streams and found that size of stable pieces of LWM increases with stream size. Their values
suggest that streams under 5 m in width require trees of about 30–35 cm in diameter to be useful
as fish habitat and to be able to persist as stable LWM in the channel. Streams of about 10 m in
width require larger trees of about 45 cm (1.5 ft) in diameter. In a basin in which over 50% of the
forest had been logged in the past 20 years, House and Boehne (1986) found that the reduction of
large conifers in the riparian zone resulted in only 0.4 pieces per 100 m of LWM large enough to
influence channel morphology. Rosenfeld and Huato (2003) found that the proportion of wood
material that formed pools increased from 6% for pieces with a diameter of 15–30 cm to 43% for
pieces with a diameter of more than 60 cm. Large woody material more than 60 cm in diameter
formed a higher proportion of pools across all channel widths. A simple, size-structured model of
LWM abundance in small streams suggests that loss of LWM larger than 60 cm in diameter will
greatly decrease pool frequency across all channel widths but have the greatest impact on large
streams. While these studies are more related to the Pacific Northwest, they do demonstrate the
lack of quantity and quality of LWM within the Scott River Watershed.
The results of this work on spawning substrate quantity and quality suggest that while there is
extensive quality habitat for coho spawning there are also numerous areas where improvements
74
can be made. Specifically, there is an overall lack of LWM and an over-abundance of confined
channels in the lower watershed.
Use of the Scott River Spawning Habitat Management Plan
This Plan provides watershed stakeholders with a framework for identifying, quantifying and
qualifying spawning habitat for anadromous salmonids within the Scott River Basin and for
prioritizing and strategizing the protection and maintenance of quality habitat as well as
enhancement of sub-optimal habitat. The goal of this document is to provide management tools
that support the coexistence of a productive, viable basin fishery, a healthy economy, and a
quality of life for the community of the Scott River Basin. The Plan is envisioned as a living
document that will continue to be refined as river restoration moves forward, more scientific
information on Scott River salmonids is gathered, and more stakeholder outreach activities have
been completed and documented.
Priorities for Spawning Gravel Management
The hierarchical strategy we present is based on six elements: (1) principles of watershed
physical processes, (2) identifying existing high-quality habitats, (3) identifying and prioritizing
compromised habitats that otherwise meet general spawning requirements of native salmonids,
(4) current knowledge of the effectiveness of specific enhancement techniques, (5) long-term
monitoring, and (6) adaptive management. Following a watershed assessment, efforts should
focus on protecting areas with intact processes and high-quality habitat. Secondly, potential
spawning reaches should be identified and prioritized as to their level of impairment and what
techniques can be used to enhance substrate quality and habitat morphology within impaired
reaches (Figure 39). As enhancement is implemented, monitoring should identify what works
and what does not. Techniques that do not function well should be avoided and new techniques
should be implemented under the process of adaptive management (see below).
It is important to note that this Plan focuses on quantity and quality of spawning gravels and
augmentation of sediment and structure. These are short-term fixes. Spawning gravel
management should be incorporated into an overall watershed management plan that also
focuses on reconnecting isolated high-quality fish habitats, such as instream or off-channel
habitats made inaccessible by artificial obstructions, as well as restoring hydrologic, and riparian
processes (Roni et al. 2002).
75
Habitat meets the requirements of
spawning and incubating salmonids
(see Chart 1)
Chart 3
Yes
Not potential spawning
habitat;
No need for further
assessment
Spawning habitat is of high
quality (see Chart 2)
No
Yes
No
Appropriate for
enhancement?
Continue to monitor
Yes
No
Decide enhancement
action
No
No
Action performed?
Yes
Yes
Yes
Implemented as planned?
Effective at improving
habitat?
Adaptive management
No
Figure 39. Prioritization planning for monitoring and enhancement of salmonid spawning habitat.
Identify, Designate and Protect Functional Spawning Habitat
It is recommended that the assessment process we outline above be used to identify and
designate strategic habitat areas for the maintenance of spawning populations of Scott River
salmon and steelhead (emphasizing coho salmon). At present, French Creek appears to provide
some of the best available habitat for coho salmon spawning and incubation. While it lacks
appropriate levels of LWM (similar to the entire watershed) the stream has a high probability for
being open during the coho spawning season. The ~ 9500 m stretch of French Creek,
encompassed by Reaches 1 through 3, has a gradient that is medium to high preference and bed
substrate sizes preferred by coho salmon. Low fine sediment concentrations throughout this
stream segment indicate conditions for relatively high estimated embryo survival. Reach 1 also
has some of the highest recorded coho redd numbers in the watershed.
Identify, Designate and Prioritize Impacted Spawning Habitat for Enhancement
The prioritization scheme identified 10 reaches which ranked medium to high for potential
enhancement or rehabilitation through gravel augmentation or structural enhancement. It is
important to note that in a dynamic watershed such as the Scott River, rankings will most likely
76
change over time due to management implementation and general evolution of the watershed in
relationship to anthropogenic and natural disturbance.
Finalize and implement a long-term monitoring and enhancement program
In addition to identifying enhancement sites we make the following recommendations:
1. We believe that a long-term monitoring program should be run through the RCD to
ensure standardized, quality monitoring occurs. However, there should be an oversight
committee that directs the monitoring program, makes suggestions on how to track and
improve monitoring and helps prioritize restoration implementation.
2. In order for the monitoring program to be effective, data require spatial analysis and such
information should be kept together in one location. The database should be regularly
backed up and stored at another facility.
3. Data collection should be expanded to areas of the watershed that were not accessed
during this process, including sampling and classification of reach scale habitat.
4. The gradient model should be refined to incorporate “edge-effect” associated with delta
formation at the mouths of tributaries. The mouth of Tompkins and Canyon creeks are
examples of this.
5. The gravel size model should better define reach variation that might be obscured under
the present monitoring scheme. The South Fork Scott River is an example.
6. Continue flow discharge monitoring on tributary reaches and expand coverage to the East
side of the Valley (i.e. Moffett Creek).
7. Monitor slope and cross section changes at study sites.
Limitations
The Plan only provides a framework for the assessment of two components of salmonid
lifehistory, spawning and incubation habitat. In general, much of what occurs on the Scott River
is uniquely related to what happens in the Klamath River watershed and there are many issues
impacting salmonid spawning resources of the Scott River that are outside the scope of this
study. For instance, the water quality of the Scott River and its tributaries was listed as
“impaired” for sediment and temperature, under Section 303(d) of the Clean Water Act, by the
North Coast Regional Water Quality Control Board and the US EPA and are targeted for
nonpoint source management. Temperature issues include: 1) solar heat load (i.e., sunlight) at
streamside (riparian) locations in the Scott River Watershed; 2) heat load from tailwater return
flows; and, 3) reduced assimilative capacity from surface water flow reductions. Inadequate
streamflow is a commonly identified problem of the Scott River, particularly in Scott Valley, and
it directly affects other local water quality problems, such as high temperature and nutrient
levels, primarily during the summer (Quigley 2008). Low flows in the Scott River and tributaries
have caused poor holdover of adult salmon until spawning, blocked access to upstream spawning
areas, and reduced availability of spawning sites. Coho salmon in the region were listed as
77
threatened under the federal Endangered Species Act in 1997 by the National Marine Fisheries
Service. This listing increases the need to understand and improve the quality of coho salmon
habitat in the Scott River system.
To function properly, this Plan should be incorporated as part of a broader strategy, including
longterm economic and life quality issues for the people of the Scott Valley community, water
quality management, riparian vegetation management, flood protection, permitting programs and
Klamath Watershed management plans. This includes collaboration with Klamath River
programs.
Adaptive Management
Employment of an adaptive management strategy will increase the effectiveness of restoration
actions and address scientific uncertainty. Adaptive management is an approach that allows
resource managers and watershed stakeholders to learn from past experiences through formal
experiment or by altering actions based on their measured effectiveness. Monitoring programs
are the foundation of the adaptive management approach. Adaptive management is the planning,
design, implementation, and monitoring of restoration projects to address the important questions
regarding their success and longevity. The concept of adaptive management is to acknowledge
uncertainty about the way natural systems function and, how best to achieve desired restoration
goals, in the face of this uncertainty. Adaptive management helps refine the actions necessary to
meet certain restoration objectives based on robust data acquired from monitoring. It is learningbased management (MacDonald et al. 2007). Results are used to evaluate whether different
restoration actions were effective at achieving specified goals, and to update knowledge and
adjust restoration actions (MacDonald et al. 2007) (Figure 40).
Assess
Problem
Design
Implement
Adjust
Evaluate
Monitor
Figure 40. Basic flow diagram of adaptive management activities.
Research, monitoring, and evaluation are central to adaptive management, and implementation of
these activities is how the science-management interface is informed (Magnuson et al. 1996).
MacDonald et al. (1991) defines several types of monitoring including Implementation
Monitoring which determines if the proposed action was implemented as planned, and
Effectiveness Monitoring which determines if the proposed action had the desired effect.
78
Outreach
Restoration planning is generally more effective when it includes public participation and
support (AMFSTP 2002). Local communities are often the best stewards of their environment,
and can be engaged through outreach activities that encourage participation with local projects,
including planning and monitoring. We recommend that the users of this document engage the
local community in the restoration planning process, and potential feedback mechanisms that
would allow for community participation and involvement. The primary target audience for
outreach will include residents of local communities of the Scott River Watershed, recreational
users, local government agencies, timber and agricultural interests, non-profit environmental and
recreational organizations, and the irrigation and water districts that obtain water from the river.
The Scott River Watershed Council and the Siskiyou Resource Conservation District can provide
critical links between land owners, other stakeholders, including the public (resource agencies)
and private sectors (Griffin 2007). A variety of other tools may also be used including public
meetings to present and discuss the Plan and planning process, newspaper articles, and a project
website where interested parties may get contact information, download support materials, and
give feedback.
River restoration has value in its ability to recover essential fish habitats, but also in its ability to
restore important ecosystem processes that may contribute to an improved environment (Loomis
et al. 2000). For instance, by restoring and improving functional side channels and floodplains,
these actions may also benefit flood control and improve water and air quality among other
benefits. These areas may also provide services such as groundwater recharge, nutrient
exchange, prey resource production, and improved aesthetics (e.g., native plant communities),
thereby improving the quality of life for the local community with the restoration process. When
these goals become synonymous with salmonid habitat enhancement, managers improve the
ability to communicate with, and garner support from, the local community.
ACKNOWLEDGEMENTS
This project was funded by a grant through the Pacific States Marine Fisheries Commission. We are
indebted to the numerous landowners that allowed us access to the Scott River through their homes and
properties. Without them, this document would not be possible. The people we met were friendly and
interested in our work and it made for a wonderful experience and facilitated our ability to collect quality
data for this study. We are grateful to the numerous scientists that have carried out research in the Scott
River and adjacent watersheds which provided a framework and guidance for our research. We also
gratefully acknowledge the authors of the published science and research that is the backbone of this
project. We thank C. Burr, T. Kennedy, M. Kirsten, J. Montgomery, K. Munson, N. Retford, B. Walsh,
C. Watry and all of the staff and field personnel that provided quality data collection, laboratory work and
data analysis for this study. We thank K. Vyverberg for review of an earlier draft of this document.
79
LITERATURE CITED
Abbe, T. B. and D. R. Montgomery. 1996. Large woody debris jams, channel hydraulics and
habitat formation in large rivers. Regulated Rivers Research and Management 12: 201221.
Adaptive Management Forum Scientific and Technical Panel (AMFSTP). 2002. Merced River
Adaptive Management Forum Report. Report prepared for the Central Valley Project
Improvement Act Anadromous Fish Restoration Program and the CALFED Bay-Delta
Program. 19 July 2002. University of California, Davis. (Available:
http://www.delta.dfg.ca.gov/afrp/documents/MERCED_RIVER_AMF_REPORT.pdf).
Allen, M. A., and T. J. Hassler. 1986. Species profiles: life histories and environmental
requirements of coastal fishes and invertebrates (Pacific Southwest)-Chinook salmon.
U.S. Fish and Wildlife Service Biological Report 82(11.49). U.S. Army Corps of
Engineers, TR EL-82-4. 26 pp.
Barnhart, R. A. 1986. Species profiles: life histories and environmental requirements of coastal
fishes and invertebrates (Pacific Southwest)—steelhead. U.S. Fish and Wildlife Service
Biological Report 82(11.60). U.S. Army Corps of Engineers, TR EL-82-4. 21pp.
Bauer, S. B., and T. A. Burton. 1993. Monitoring protocols to evaluate water quality effects of
grazing management on western rangeland streams. U.S. Environmental Protection
Agency, Water Division, Surface Water Branch, Region 10, Seattle, WA. pp. 145-148.
Bilby, R. E., and J. W. Ward. 1989. Changes in characteristics and function of woody debris with
increasing size of streams in western Washington. Transactions of the American Fisheries
Society 118: 368-378.
Bisson, P. A., J. L. Nielsen, R. A. Palmason, and L. E. Grove. 1981. A system of naming habitat
types in small streams, with examples of habitat utilization by salmonids during low
stream flow. Pp. 62-73 in: N. B. Armantrout, Ed. Symposium on acquisition and
utilization of aquatic habitat inventory information. American Fisheries Society, Portland,
Oregon, USA.
Black, G. 1998. Scott River Corridor Habitat Improvement Project Located at The Eiler Ranch.
Agreement # 14-48-0001-96672. Project Identification #96-JITW-02. Siskiyou Resource
Conservation District. P.O. Box 268 Etna, CA 96027. 12 pp.
Buffington, J. M., D. R. Montgomery, and H. M. Greenberg. 2004. Basin-scale availability of
salmonid spawning gravel as influenced by channel type and hydraulic roughness in
mountain catchments. Canadian Journal of Fisheries and Aquatic Sciences 61:2085-2096.
Caamaño, D., P. Goodwin, J. M. Buffington, J. C. P. Liou, and S. Daley-Laursen. 2009. Unifying
Criterion for the Velocity Reversal Hypothesis in Gravel-Bed Rivers. Journal of
Hydraulic Engineering 135.
Cadenasso, M.L., S.T.A. Pickett, K.C. Weathers, and C.G. Jones. 2003. A framework for a
theory of ecological boundaries. BioScience 53:750-758.
CDFG. 1978. 1978 aerial king salmon redd count. California Department of Fish and Game,
Reg. 1, 2 pp.
CDFG. 1979. 1979 Aerial king salmon redd counts. California Department of Fish and Game,
Reg. 1, 2 pp.
CDFG. 1983. 1983 Aerial king salmon redd counts. California Department of Fish and Game,
Reg. 1, 2 pp.
CDFG. 1997. A Biological Needs Assessment for Anadromous Fish in the Shasta River,
Siskiyou County, California. CDFG, Region 1. Northern Management Area. Redding,
CA. 29 pp.
80
Clawson, R. F., D. J. Cahoon, and J. M. Lacey. 1986. Shasta/Klamath Rivers Water Quality
Study. For CA Department of Water Resources Northern District. Sacramento, CA. 69
pp.
Constantine, C.R., J.F. Mount, and J.L. FLorsheim. 2003. The effects of longitudinal differences
in gravel mobility on the downstream fining pattern in the Cosumnes River, California.
The Journal of Geology 111:233-241.
Coots, M. 1957. Shasta River, Siskiyou County, 1955 king salmon count, and some notes on the
1956 run. California Department of Fish and Game, Inland Fisheries, Br. Admin. Rept.
No 57-5. 6 p.
Cowardin, L. M., V. Carter, F. C. Golet, and E. T. LaRoe. 1979. Classification of wetlands and
deepwater habitats of the United States. U.S. Department of the Interior, Fish and
Wildlife Service, Washington, DC. Version 04DEC98. (Available:
http://www.npwrc.usgs.gov/resource/1998/classwet/classwet.htm).
Crandell, D. R. 1989. Gigantic Debris Avalanche of Pleistocene Age From Ancestral Mount
Shasta Volcano, California, and Debris-Avalanche Hazard Zonation. U.S. Geological
Survey Bulletin 1861. Denver, CO. 32 pp.
DWR (California Department of Water Resources). 1991. Scott River Flow Augmentation
Study. State of California. The Resources Agency. Department of Water Resources
Northern District. Cooperative Agreement 14-16-89521 between U.S. Fish and Wildlife
Service and The California Department of Water Resources. 137 pp.
Effron, B., and G. Gong. 1983. A leisurely look at the bootstrap, the jackknife, and crossvalidation. The American Statistician 37:36-48.
Elkins, E. M., G. B. Pasternack, and J. E. Merz. Use of slope creation for rehabilitating incised,
regulated, gravel bed rivers. Water Resources Research 43.
ESA. 2008. Shasta River Watershed-Wide Permitting Program. Prepared for the California
Department of Fish and Game.
Fuller, D. D. 1990. Seasonal utilization of instream boulder structures by anadromous salmonids
in Hurdygurdy Creek, California. Fish Habitat Relationship Technical Bulletin No. 3,
U.S. Department of Agriculture, Washington, D.C., USA.
Gaeuman, D. A., J. C. Schmidt, and P. R. Wilcock. 2003. Evaluation of in-channel gravel storage
with morphology-based gravel budgets developed from planimetric data. Journal of
Geophysical Research 108:1-16.
Geist, D. R., and D. D. Dauble. 1998. Redd site selection and spawning habitat use by fall
chinook salmon: The importance of geomorphic features in large rivers. Environmental
Management 22:655-669.
Griffin, C. B. 2007. Watershed councils: an emerging form of public participation in natural
resource management. Journal of the American Water Resources Association 35:505518.
Gwynne, B. 1993. Investigation of Water Quality Conditions in the Shasta River, Siskiyou
County. Interim Report for California Regional Water Quality Control Board. Santa
Rosa, CA. 26 pp.
Harmon, M. E., Franklin, J. F., Swanson, F. J., Sollins, P., Gregory, S. V., Lattin, J. D.,
Anderson, N. H., Cline, S. P., Aumen, N. G., Sedell, J. R., Lienkaemper, G. W.,
Cromack, K. Jr and Cummins, K. W. 1986. ‘Ecology of coarse woody debris in
temperate ecosystems’, Advances in Ecological Research, 15, 133–302.
Hassler, T. J. 1987. Species profiles: Life histories and environmental requirements of coastal
fishes and invertebrates (Pacific Southwest)- Coho salmon. U.S. Fish and Wildlife
Service Biological Report 82(11.70). U.S. Army Corps of Engineers, TR EL-82-4. 19 pp.
81
House, R. A., and P. L. Boehne. 1986. Effects of instream structures on salmonid habitat and
populations in Tobe Creek, Oregon. North American Journal of Fisheries Management 6:
38-46.
House, R., and P. Boehne. 1985. Evaluation of instream enhancement structures for salmonid
spawning and rearing in a coastal Oregon stream. North American Journal of Fisheries
Management 5:283-295.
Jong, H. W. 1994. Chinook Salmon Spawning Habitat Quality Evaluation Studies on the Shasta
River and South Fork Trinity River Basins. CA Department of Fish and Game, Natural
Stocks Assessment Project. Arcata, CA. 47 pp.
Jong, H. W. 1997. Evaluation of Chinook spawning habitat quality in the Shasta and South Fork
Trinity rivers, 1994. California Department of Fish and Game, Inland Fisheries Admin.
Report 97. 23 pp.
Kondolf, G. M. 1998. Some suggested guidelines for geomorphic aspects of anadromous
salmonid habtiat restoration proposals. A Report to the United States Fish and Wildlife
Service, 4001 N Wilson Way, Stockton, CA.
Lambeck, R. J. 1997. Focal Species: A Multi-Species Umbrella for Nature Conservation.
Conservation Biology 11:849-856
Lisle, T. E., and R. E. Eads. 1991. Methods to measure sedimentation of spawning gravels.
Mann, M.P., Rizzardo, Julé, and Satkowski, Richard, 2004, Evaluation of methods used for
estimating selected streamflow statistics, and flood frequency and magnitude, for small
basins in north coastal California: U.S. Geological Survey Scientific Investigations
Report 2004-5068, 92 p.
May, C. L., B. Pryor, T. E. Lisle, and M. M. Lang. 2007. Assessing the risk of redd scour on the
Trinity River. Report prepared for the Bureau of Reclamation, Trinity River Restoration
Program, Weaverville, CA. 63 pp.
McNeil, W. J., and W. H. Ahnell. 1964. Success of pink salmon spawning relative to size of
spawning bed materials. U.S. Fish and Wildlife Service, Special Science Report for Fish
469. 15 pp.
Merz J. E., J. R. Smith, M. L. Workman, J. D. Setka, and B. Mulchaey. 2008. Aquatic
macrophyte encroachment in Chinook salmon spawning beds: lessons learned from
gravel enhancement monitoring in the lower Mokelumne River, California. North
American Journal of Fisheries Management 28:1568–1577.
Merz, J. E., and J. D. Setka. 2004. Riverine habitat characterization of the lower Mokelumne
River, California. Report to the Federal Energy Regulatory Commission from East Bay
Municipal Utility District, 1 Winemasters Way, Suite K, Lodi, CA 95240.
Merz, J. E., G. B. Pasternack, and J. M. Wheaton. 2006. Sediment budget for salmonid spawning
habitat rehabilitation in a regulated river 76:207-228.
Merz, J. E., J. D. Setka, G. B. Pasternack, and J. M. Wheaton. 2004. Predicting benefits of
spawning habitat rehabilitation to salmonid (Oncorhynchus spp.) fry production in a
regulated California river. Canadian Journal of Fisheries and Aquatic Sciences 61:1-14.
Meixler, M.S., M.B. Bain, and M. T. Walter. 2009. Predicting barrier passage and habitat
suitability for migratory fish species. Ecological Modeling 220:2782–2791.
Montgomery, D. R., and J. M. Buffington (1997), Channel-reach morphology in mountain
drainage basins, Geol. Soc. Am. Bull., 109, 596– 611.
Montgomery, D. R., Buffington, J. M., Smith, R. D., Schmidt, K. M., and Pess, G., 1995, Pool
spacing in forest channels. Water Resources Research, v. 31, p. 1097–1105.
Mount, J.F., P.B. Moyle, and S.M. Yarnell. 2003. A study of juvenile salmonid habitat in select
Scott River Tributaries. Final Report. Sponsored by the University of California
82
Presidential Chair in Undergraduate Education and the Roy Shlemon Chair in Applied
Geosciences. University of California, Davis, CA. 108 pp.
Mundie, T. R. 1974. Optimization of the salmonid nursery stream. Journal of the Fisheries
Research Board of Canada 31:1827-1837.
Nawa, R. K., and C. A. Frissell. 1993. Measuring scour and fill of gravel streambeds with scour
chains and sliding-bead monitors. North American Journal of Fisheries Management
13:634-639.
NCIRWMP, 2007. (Available:http://www.northcoastirwmp.net/Content/10301/preview.html).
Parker, G. 1990. Surface-based bedload transport relation for gravel rivers. Journal of Hydraulic
Research 28:417–436.
Pasternack, G. B. 2008. Spawning habitat rehabilitation: advances in analysis tools. In D. A.
Sear, P. DeVries, and S. Greig, Eds. Salmonid spawning habitat in rivers: physical
controls, biological responses, and approaches to remediation. Symposium 65, American
Fisheries Society, Bethesda, MD.
Pasternack, G. B., C. L. Wang, and J. E. Merz. 2004. Application of a 2D hydrodynamic model
to design of reach-scale spawning gravel replenishment on the Mokelumne River,
California. River Research and Applications 20:205-225.
Peterman, R. M. 1990a. Statistical power analysis can improve fisheries research and
management. Canadian Journal of Fisheries and Aquatic Sciences 47:2-15.
Peterman, R. M. 1990b. The importance of reporting statistical power: the forest decline and
acidic deposition example. Ecology 71:2024-2027.
Pitlick, John; Cui, Yantao; Wilcock, Peter. 2009. Manual for computing bed load transport using
BAGS (Bedload Assessment for Gravel-bed Streams) Software. Gen. Tech. Rep. RMRSGTR-223. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky
Mountain Research Station. 45 p.
(PDF File Size: 2.10 MB)
Quigley, D. 2005. Prepared by the Siskiyou RCD for the U.S> Fish and Wildlife Service
Agreement #113333JO27 and California Department of Fish and Game Agreement
#PO310331. SQRCD. P.O. Box 268, Etna, CA 96027.
Quigley, D. 2008. Scott River Watershed Monitoring Program- Water Quality. Water
Temperature Monitoring and Sediment Sampling and Analysis 2005, 2006, and 2007.
Prepared by the Siskiyou RCD for the California Department of Fish and Game
Agreement #PO410336. SQRCD. P.O. Box 268, Etna, CA 96027.
Quigley, D. 2003. Stream inventory report. Scott River Watershed. Siskiyou RCD. State Water
Resources Control Board – Proposition 13 Cooperative Agreement #01-139-251-0. and
the US Fish and Wildlife Service. 100 pp.
Quinn, T. P. 2005. The Behavior and Ecology of Pacific Salmon and Trout. University of
Washington Press.
Raleigh, R. F., W. J. Miller, and P. C. Nelson. 1986. Habitat suitability index models and
instream flow suitability curves: Chinook salmon. U.S. Fish and Wildlife Service
Biological Report 82(10.122), 64 pp.
Rantz, S.E., 1969, Mean annual precipitation in the California Region: U.S. Geological Survey
Open-File Map (reprinted 1972, 1975).
Rantz, SE. 1968. Average Annual Precipitation and Runoff in North Coastal California Map.
HA-298. United States Geological Survey.
Ricker, S. J. 1997. Evaluation of salmon and steelhead spawning habitat quality in the Shasta
River Basin, 1997. Inland Fisheries Administrative Report No. 97-9. Carpenter, R. M.
Ed. California Department of Fish and Game, Region 1, 1416 9th Street, Sacramento,
CA.
83
Rogers, D. W. 1975. Field note: Shasta River. California Dept. Fish.
Roni, P., T.J. Beechie, R.E. Bilby, F.E. Leonetti, M.M. Pollock, and G.R. Pess. 2002. A review
of stream restoration techniques and a hierarchical strategy for prioritizing restoration in
Pacific Northwest watersheds. North American Journal of Fisheries Management 22:1–
20.
Sandercock F.K. 1991. Life history of coho salmon (Oncorhynchus kisutch) In C. Groot & L.
Margolis, Eds. Pages 395-445 Pacific Salmon Life Histories. UBC Press, Vancouver.
Scott, R. G., and K. Buer. 1981. Klamath and Shasta rivers spawning gravel study. California
Department of Water Resources, Northern District, Red Bluff. 178 pp.
SCSRT (The Shasta-Scott Coho Salmon Recovery Team) 2003. Shasta and Scott River Pilot
Program for Coho Salmon Recovery: with recommendations relating to Agriculture and
Agricultural Water Use. Prepared for the California Department of Fish and Game. 125
pp.
Sedell, J. R., and F. J. Swanson. 1984. Ecological characteristics of streams in old-growth forests
of the Pacific Northwest. In W. R. Meehan, T. R. Merrell, and T. A. Hanley, Eds. Pages
9-16 Fish and wildlife relationships in old-growth forests: Proceedings of a symposium.
American Institute of Fishery Research Biologists. Portland, OR, USA.
Sedell, J. R., F. H. Everest, and F. J. Swanson. 1982. Fish habitat and streamside management:
past and present. Pages 249-255 in Proceedings of the Society of American Foresters
annual meeting. Society of American Foresters, Bethesda, Maryland.
Sedell, J. R., F. J. Swanson, and S. V. Gregory. 1984. Evaluating fish response to woody debris.
Pages 222-245 in Proceedings of the Pacific Northwest stream habitat management
workshop.
Sedell, J. R., P. A. Bisson, J. A. June, and R. W. Speaker. 1982. Ecology and habitat
requirements of fish populations in South Fork Hoh River, Olympic National Park. Pages
47-63 in: E. Starkey, editor. Ecology research in national parks of the Pacific Northwest.
Forest Research Laboratory, Oregon State University. Corvallis, Oregon, USA.
Shelton, L.R. 1994. Field guide or collecting and processing stream-water samples for the
National Water=Quality Assessment Program. U.S. Geological Survey Open-file Report
94-455. Part of Appendix D. in Surface Water Ambient Monitoring Program (SWAMP)
Quality Assurance Program. 62 pp.
Shelton, L.R., and P.D. Capel. 1994. Guidelines for collecting and processing samples of stream
bed sediment for analysis of trace elements and organic contaminants for the National
Water-Quality Assessment Program. U.S. Geological survey Open-file report 94-458.
Sacramento, California.
Snider, W. M., D. B. Chritophel, B. L. Jackson, and P. M. Bratovich. 1992. Habitat
characterization of the lower American River. Stream Flow and Habitat Evaluation
Program, Environmental Services Division, California Department of Fish and Game,
Sacramento CA.
Sommarstrom, S. 2001. Scott River Monitoring Plan. Sediment Sampling and Analysis – 2000
Final Report 2001. Prepared for the Siskiyou Resource Conservation District and Scott
River Watershed Council California Department of Fish and Game Contract Agreement
#P9985081. 50 pp.
Sommarstrom, S. 1990. Scott River Granitic Sediment Study Siskiyou Resource Conservation
District.
Sommarstrom, S., E. Kellogg, and J. Kellogg. 1991. Scott River Watershed Granitic Sediment
Study. Prepared for the Siskiyou Resource Conservation District. Funding Provided by
the Klamath River Basin Fisheries Task Force U.S. Fish and Wildlife Service
Cooperative Agreement 14-16-001-89506. 175 pp.
84
Sommers, T., D. McEwan, and R. Brown. 2001. Factors affecting Chinook salmon spawning in
the lower Feather River. In Brown, R. Ed. Contributions to the Biology of Central Valley
Salmonids. California Department of Fish and Game Fish Bulletin 179:269-297.
Steel, E. Ashley, A. Fullerton, Y. Caras, M. B. Sheer, P. Olson, D. Jensen, J. Burke, M. Maher,
and P. McElhany. 2008. A spatially explicit decision support system for watershed-scale
management of salmon. Ecology and Society 13:50. (Available:
http://www.ecologyandsociety.org/vol13/iss2/art50/)
St-Hilaire, A., D. Caissie, R. A. Cunjak, and G. Bourgeois. 1997. Spatial and temporal
characterization of suspended sediments and substrate composition in Catamaran Brook,
New Brunswick. Canadian Technical Report of Fisheries and Aquatic Sciences, No.
2165.
Stillwater Sciences. 1997. A review of coho salmon life history to assess potential limiting
factors and the implications of historical removal of large woody debris in coastal
Mendocino County.
Stillwater Sciences. 2007. Physical Modeling Experiments to Guide River Restoration Projects:
Gravel Augmentation Experiments. Final Technical Memorandum. Prepared for
CALFED Ecosystem Restoration Program (Contract No. ERP-02D-P55).
Scott River TMDL Implementation Workplan · RESOLUTION NO. R1- 2005-0113.
Tappel, P. D., and T. C. Bjornn. 1983. A new method of relating size of spawning gravel to
salmonid embryo survival. North American Journal of Fisheries Management 3:123-135.
Thompson, S. K. 1996. Sampling, Second Edition. John Wiley & Sons Inc.
USFWS (United States Fish and Wildlife Service). 1998. Klamath River (Iron Gate Dam Seiad
Creek) Life Stage Periodicities for Chinook, Coho, and Steelhead. April 1998. Prepared
by: Department of Interior U.S. Fish and Wildlife Service Coastal California Fish and
Wildlife Office Arcata, California. Funded by: U.S. Geological Survey. 51 pp.
Vignola, E., and M. Deas. 2005. Lake Shastina Limnology. Watercourse Engineering, Inc.
Davis, CA
Waananen, A.O., and Crippen, J.R., 1977, Magnitude and frequency of floods in California: U.S.
Geological Survey Water-Resources Investigations Report 77-21, 96 p.
Ward, B. R., and P. A. Slaney. 1979. Evaluation of instream enhancement structures for the
production of juvenile steelhead trout and coho salmon in the Keogh River: progress
1977 and 1978. Fisheries Technical Circular 45, Ministry of the Environment, Fish and
Wildlife Branch, Vancouver, British Columbia, Canada.
Ward, B. R., and P. A. Slaney. 1981. Further evaluations of structures for the improvement of
salmonid rearing habitat in coastal streams of British Columbia, in: T. Hassler editor.
Proceedings: Propagation, enhancement and rehabilitation of anadromous salmonid
populations and habitat symposium. Humbolt State University, Arcata, CA, USA.
Washington Department of Fish and Wildlife 2004. General Design and Selection
Considerations for Instream Structures.
Watershed Sciences, LLC. 2004. Aerial surveys using thermal infrared and color videography.
Scott and Shasta River Sub-Basins. Final Report to California North Coast Regional
Water Quality Control Board, Santa Rosa, CA and University of California, Davis, CA.
59 pp.
Weitkamp, L. A., T. C. Wainwright, G. J. Bryant, G. B. Milner, D. J. Teel, R. G. Kope, and R. S.
Waples. 1995. Status review of coho salmon from Washington, Oregon, and California.
U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-24.
West, J. R. 1984. Enhancement of salmon and steelhead spawning and rearing conditions in the
Scott and Salmon rivers, California. Pages 117-127 in Hassler (1984).
85
West, J. R., O. J. Dix, A. D. Olson, M. V. Anderson, S. A. Fox, and J. H. Power. 1990.
Evaluation of fish habitat condition and utilization in Salmon, Scott, Shasta, and midKlamath subbasin tributaries. U.S. Forest Service, Klamath National Forest, Yreka. 90
pp.
Wheaton, J. M., G. B. Pasternack, and J. E. Merz. 2004a Spawning habitat rehabilitation – I.
Conceptual approach and methods. International Journal of River Basin Management
2:3–20.
Wheaton, J. M., G. B. Pasternack, and J. E. Merz. 2004b Spawning habitat rehabilitation – II.
Using hypothesis development and testing in design, Mokelumne River, California,
U.S.A. International Journal of River Basin Management 2:21-37.
Wilcock, P. R. 1993. The critical shear stress of natural sediments. Journal of Hydraulic
Engineering 119:491–505.
Wilcock, P. R. 2001. Toward a practical method for estimating sediment transport rates in
gravel-bed rivers. Earth Surface Processes and Landforms 26:1395-1408.
Wohl, E., and D. Merritt (2005), Prediction of mountain stream morphology, Water Resour.
Res., 41, W08419,doi:10.1029/2004WR003779.
86
APPENDIX A.
FLOW ANALYSIS
Analysis of connectivity in the Scott River and Tributaries
Erich Yokel and Danielle Quigley Yokel – Siskiyou RCD
In the Scott River watershed, the combination of low precipitation (and water supply) due to a
Mediterranean climate and significant geomorphic alteration of the Scott River and portions of
the major tributaries due to legacy land use results in the loss of surface flow in stream reaches
that become disconnected from the main stem Scott River in late summer and early fall during
some water years (e.g. September and October) (Map 1). The persistence of these disconnected
reaches into the period of adult Chinook and coho migration into spawning grounds can limit the
access to otherwise available spawning habitat for these two anadromous species.
This analysis attempts to utilize discharge data collected at the USGS gaging station on the Scott
River below Fort Jones and DWR gages on Shackleford and French creeks in conjunction with
observations of the timing of connectivity during different water years to generate a better
understanding of the available universe of potential spawning grounds during the period of
Chinook and coho salmon migration. The majority of observations on tributary-main stem
connectivity have been documented in the Scott Valley since 2001 during the performance of on
the ground adult coho spawning and carcass surveys. For this reason this analysis is limited to
the water years (WY) of 2002 – 2010. Certified USGS daily mean discharge (cfs) data is
presented for WY2002 – WY2009 with preliminary discharge data presented for WY2010
(Figures 1 – 19). Discharge data is presented for the period of October 1st through January 31st
for each water year. It is believed that this period encompasses the majority of Chinook salmon
migration and the entirety of coho salmon migration in the Scott River.
I
Map 1 – Stream reaches disconnected from the Scott River due to the occurrence of subsurface
flow in the Scott Valley. Areas disconnected on an average year are denoted with solid black
line features. Areas that become disconnected during periods of drought are denoted by the white
line.
II
Figure 1 – Scott River below Scott River – daily mean discharge – 10/1/01 – 1/31/02
Figure 2 – Scott River below Scott River – daily mean discharge – 10/1/01 – 1/31/02
Figure 3 – Scott River below Scott River – daily mean discharge – 10/1/02 – 1/31/03
III
Figure 4 – Scott River below Scott River – daily mean discharge – 10/1/02 – 1/31/03
Figure 5 – Scott River below Scott River – daily mean discharge – 10/1/02 – 1/31/03
Figure 6 – Scott River below Scott River – daily mean discharge – 10/1/03 – 1/31/04
IV
Figure 7 – Scott River below Scott River – daily mean discharge – 10/1/03 – 1/31/04
Figure 8 – Scott River below Scott River – daily mean discharge – 10/1/04 – 1/31/05
Figure 9 – Scott River below Scott River – daily mean discharge – 10/1/04 – 1/31/05
V
Figure 10 – Scott River below Scott River – daily mean discharge – 10/1/04 – 1/31/05
Figure 11 – Scott River below Scott River – daily mean discharge – 10/1/05 – 1/31/06
Figure 12 – Scott River below Scott River – daily mean discharge – 10/1/06 – 1/31/07
VI
Figure 13 – Scott River below Scott River – daily mean discharge – 10/1/06 – 1/31/07
Figure 14 – Scott River below Scott River – daily mean discharge – 10/1/07 – 1/31/08
Figure 15 – Scott River below Scott River – daily mean discharge – 10/1/07 – 1/31/08
VII
Figure 16 – Scott River below Scott River – daily mean discharge – 10/1/08 – 1/31/09
Figure 17 – Scott River below Scott River – daily mean discharge – 10/1/08 – 1/31/09
Figure 18 – Scott River below Scott River – daily mean discharge – 10/1/09 – 1/27/10
VIII
Figure 19 – Scott River below Scott River – daily mean discharge – 10/1/09 – 1/27/10
Observations of connectivity, based on adult coho spawning ground surveys
Tributary
2001
2002
2003
Scott Tailings
East Fork and South Fork
*12/4
2004
no connectivity issue connected by
11/29/04
always connected
Sugar Creek
always connected
always connected
Wildcat Creek
not before 11/22
15-Dec
no connectivity issue
French Creek
not before 11/22
15-Dec
no connectivity issue
Etna Creek
not before 11/22
15-Dec
unk
6-Dec
Patterson (Etna)
not before 11/22
15-Dec
unk
6-Dec
Kidder Creek
not before 11/22
15-Dec
Moffet Creek
8-Jan-02
27-Dec
not before 11/22
*12/12
did not connect during spawning
27-Dec
early January
27-Dec
8-Dec
6-Dec
Not connected as of Not connected as of
Jan 9, 04
Jan 16, 05
Not connected as of Not connected as of
Jan 9, 04
Jan 16, 05
not before 11/22
27-Dec
Not connected as of Not connected as of
Jan 9, 04
Jan 16, 05
Shackleford Creek
Indian Creek
Rattlesnake Creek
Patterson (Fort Jones)
* spawning oberved
Table 1 – Periods and dates of connectivity for 2001 - 2004
IX
always connected
always connected
6-Dec
Not connected as of Not connected as of
Jan 9, 04
Jan 16, 05
Observations of connectivity, based on adult coho spawning ground surveys
Tributary
Scott Tailings
2005
2006
2007
no connectivity issue
2008
2009
Connected between 11/5 11/11
By Oct 19th
East Fork and South Fork
always connected
always connected
always
connected
always connected
always connected
Sugar Creek
always connected
always connected
always
connected
always connected
always connected
Wildcat Creek
French Creek
no connectivity issue
By Oct 19th
By Oct 26th
12/16 flood event
By Oct 19th
21-Dec
Patterson (Etna)
12/16 flood event
By Oct 19th
Kidder Creek
12/16 flood event
By Oct 19th
Moffet Creek
12/16 flood event
not connected as of Jan 12,
2007
Indian Creek
12/16 flood event
Rattlesnake Creek
12/16 flood event
by Nov 14
not connected as of Jan 12,
2007
not connected as of Jan 12,
2007
12/16 flood event
not connected as of Jan 12,
2007
Patterson (Fort Jones)
* spawning observed
*Nov 9
by Nov 14
unknown
Etna Creek
Shackleford Creek
*Nov 9
By Oct 19th
early March 2009
22-Dec
unk
unk
By Oct 19th
intermittent, 12/2?
unk
unk
31-Dec
not connected as of Jan
29, 2010
21-Dec
not connected as of Jan
29, 2010
not connected as of Jan
29, 2010
unk
Table 2 - Periods and dates of connectivity 2005 – 2009
Scott River Main Stem – Fort Jones Reach
During periods of low water supply in the Scott River Watershed the main stem of the Scott
River surface flow is lost in areas of the low gradient channel of the valley. This disconnected
channel has been documented to persist into October during the period of Chinook migration
impeding the migration of Chinook to their spawning grounds in the Scott Valley. It is believed
that a flow of approximately 30 – 35 cfs at the USGS gage below Fort Jones (RM – 21) is
necessary to allow volitional access to the Chinook spawning grounds between Fay Lane and the
mouth of Etna Creek. These flows were not met during the Chinook migration of 2001 (Figure
20) a year in which all Chinook spawning was limited to the bottom 7 miles of the Scott River
Canyon due to the persistence of very low flows (less than 10 cfs at the USGS gage) until the
occurrence of a series of precipitation events from 11/10 - 11/21/2001 (totaling ~ 3 inches). The
relatively strong cohort of adult coho salmon was attempting to migrate into the Scott Valley
during this period of 2001. Several observations of adult coho salmon holding in locations of the
Scott River’s canyon led to the hypothesis that the persistence of these low flows into middle
November created low flow passage barriers to adult coho migration (Mauer, 2002). Low flows
of this nature have not been seen at the USGS gage since the 2001 event.
The flow at the USGS gage and the extent of disconnected channel in the Scott River on October
1st, 2009 was roughly equivalent to that observed on October 1st, 2001 (Figure 21). Flows in the
Scott River at the gage were less than 10 cfs until a precipitation event occurring on Oct. 13th and
14th restored surface flow connectivity to the Scott River through the Fort Jones reach. This
connectivity allowed for the migration of Chinook salmon into the spawning grounds of the Scott
Valley. These two years with limited early fall water supply were used to illustrate two scenarios
for salmon migration to the spawning grounds in the Scott Valley. In 2001, sustained
precipitation and connectivity did not occur until mid-November blocking the migration of
X
Chinook salmon to the valley reaches and potentially impeding the migration of coho salmon. In
2009, a single precipitation event in mid October generated surface flow in the Scott River and a
period of flow greater than 30 cfs at the USGS gage allowing for migration of Chinook to the
valley reaches. These examples demonstrate the necessity of a significant precipitation event to
generate connectivity and/or sufficient flows to allow for the migration of adult salmon to the
Scott Valley and tributaries.
cfs
200
USGS - Scott River below Fort Jones
WY2002
150
100
daily mean cfs
50
0
10/1/2001
10/22/2001
11/12/2001
12/3/2001
12/24/2001
date
Figure 20 – Discharge at the USGS gage below Fort Jones – Oct. 1st – Dec. 31st, 2001
cfs
200
USGS - Scott River below Fort Jones
WY2010 - provisional data
150
daily mean cfs
100
50
0
10/1/2009
10/22/2009
11/12/2009
12/3/2009
date
12/24/2009
Figure 21 - Discharge at the USGS gage below Fort Jones – Oct. 1st – Dec. 31st, 2009
Adult coho salmon spawning ground surveys have been performed in the Scott River Watershed
since the fall of 2001 and we have observed the timing of coho entry and spawning in the Scott
Valley and tributaries is driven by the late fall water supply and instream flow regime (Table 3 Quigley, 2006).
XI
Table II. Spawning Timing
2001/2002
2002/2003
2003/2004
2004/2005
2005/2006
Ist Coho (Live)
observation
1st Significant Flow
Event
Nov 21
Nov 20
Dec 16
Oct 25
Oct 27
11/22 ,12/7,12/14
4-Dec
7-Dec
12/8,12/14
11/15, 11/26
Peak Spawning Period
12/20-1/2
12/18-12/20
12/1-1-7
12/13-12/24
11/30-12/08
st
th
th
th
th
Note: 2004-2005 was the first year the a concerted effort was made during Adult
Chinook Surveys to identify live coho salmon.
Table 3 – Excerpt from Quigley, 2006 – coho observations and significant flow events
Scott River Tailing Pile –
The upper reach of the main stem Scott River is confined on both banks by tailings piles created
by large scale dredging from the mid 1930’s to the mid 1950’s. The tailings piles start
downstream of the confluence of the South and East Forks at Callahan and extend for
approximately five miles to a location about 1 mile above Fay Lane. A significant reach of the
Scott River through the tailings piles loses surface flow during the average low flow period of
late summer and early fall. This area of disconnection extends from below Sugar Creek to the
end of the tailings piles where surface flow is restored. This disconnected reach of the main stem
prohibits access to several major tributaries with potential coho spawning habitat: East Fork
Scott River, South Fork Scott River, Wildcat Creek and Sugar Creek. Because surface flow
through the tailings pile reach is regularly observed to occur before adult coho salmon migrate to
the Scott Valley, there has been no imperative for the Siskiyou RCD to document the date and
flow regime at which this occurs. The tributaries above the disconnected reach through the
tailings piles have no connectivity issues that block access.
It was observed in 2007 that the tailings pile reach connected by October 19th. A storm event
created a runoff event in the Scott River that peaked at approximately 800 cfs at the USGS gage
on October 20th (Figure 14 and 15). In 2009, the tailing pile reach connected during the runoff
event following a significant precipitation event on October 13th through 14th and then
disconnected until connectivity returned sometime from Nov. 5th to 11th. Inspection of the mean
daily discharge at the USGS gage below Fort Jones (Figure 22) shows the discharge exceeding
30 cfs during the runoff event in October and then subsiding to below 30 cfs until November 5th.
After November 5th the discharge increases to greater than 40 cfs. This indicates that the tailings
pile reach was connected when there was greater than 30 cfs of discharge at the USGS gage in
2009. If this is the case in all water years and water supply regimes, the tailings pile reach
becomes connected at approximately the same flow regime at the USGS gage that is required for
the volitional migration of adult salmon to the Scott Valley. If the same flow regime is required
to remove the bottleneck to migration into the Scott Valley and above the tailings pile reach then
the tailings pile reach is not impeding migration of adult salmon. There are two complications to
the last assertion: 1) potential groundwater recharge and flow attenuation between the tailings
pile and the USGS gage and 2) the potential that Youngs Dam (the diversion structure for the
Scott Valley Irrigation District) does not volitionally pass adult salmon when the USGS gage is
at 30 – 40 cfs. These two complications, exacerbated in years with low water supply (e.g. 2009),
are not fully understood and require further investigation. In summary, it is hypothesized that the
disconnected reach through the tailings pile area of the Scott River reconnects at approximately
the same discharge magnitude at which adult salmon are able to access the Valley reach
downstream.
XII
cfs
50
USGS - Scott River below Fort Jones
WY2010 - provisional data
40
daily mean cfs
30
20
10
.
0
date
10/1/2009 10/8/2009 10/15/200 10/22/200 10/29/200 11/5/2009 11/12/200
9
9
9
9
cfs
50
USGS - Scott River below Fort Jones
WY2010 - provisional data
40
daily mean cfs
30
20
10
0
date
10/1/2009 10/8/2009 10/15/200 10/22/200 10/29/200 11/5/2009 11/12/200
9
9
9
9
Figure 22 – Provisional mean daily discharge at USGS gage 10/1 – 11/15/09
The tailing pile reach has never been disconnected into the period of adult coho salmon
migration during the period of spawning ground surveys (2001 – 2009). Adult coho were
observed spawning in the tailing reach during the beginning of the observed spawning activity
(late November) of 2004. It is not known if this main stem spawning was volitional or due to
insufficient attractor flows in the tributaries (e.g. East Fork and South Fork), see Figure 23. The
magnitude of discharge required to allow volitional migration of adult salmon to the South and
cfs
USGS - Scott River below Fort Jones
WY2005
150
140
130
120
110
100
90
80
70
60
50
40
30
20
10
0
10/1/2004
daily mean cfs
10/15/2004
10/29/2004
11/12/2004
East Fork is unknown.
Figure 23 – Mean daily discharge at USGS gage 10/1 – 12/7/04
Mouth of Shackleford Creek XIII
11/26/2004
date
The confluence of Shackleford Creek with the Scott River loses surface flow connection during
the average low flow period of late summer and early fall (Picture 1). Spawning ground surveys
performed in Shackleford Creek in the 1980’s documented significant utilization of this tributary
by adult Chinook salmon (West, unpublished data). Chinook salmon were observed spawning in
the lower reach of Shackleford Creek in 2006 and 2007 when connectivity was achieved at the
mouth during the period of migration. A significant population of Chinook spawns in the main
stem Scott River in the vicinity of the confluence with Shackleford Creek. Shackleford Creek
and Mill Creek (a major tributary) offer both suitable spawning habitat and rearing habitat for
adult and juvenile salmonids.
Picture 1 – Mouth of Shackleford 12/23/09
The California Dept. of Water Resources (DWR) has operated a stream gage above the mouth of
Shackleford Creek since 2004. DWR has documented that it takes approximately 15 – 18 cfs of
discharge to generate surface flow connectivity at the mouth of Shackleford Creek and
approximately 25 cfs is required to generate a flow of 10 cfs at Shackleford’s confluence with
the Scott River. It is hypothesized by DWR and accepted by Cal. Dept. of Fish and Game that
approximately 25 cfs at the gage is required to generate sufficient flows for volitional access to
Shackleford Creek. This criterion will be used to access the timing of sufficient connectivity for
Shackleford Creek from WY2005 – 2008 (the period of certified data currently available)
(Figures 24 – 27). In most years, the first significant precipitation event creates a runoff event
that peaks well in excess of the 25 cfs threshold at the DWR gage on Shackleford Creek and the
flow maintains above this threshold for the period of coho migration (WY2005 – 2007 Figure 24
– 26).
XIV
cfs
100
90
Shackleford Creek - daily mean discharge WY2005
80
70
daily
mean
25 cfs
60
50
40
12/7/04
30
↘
20
10
0
10/1/2004
10/22/2004
11/12/2004
12/3/2004
date
12/24/2004
1/14/2005
Figure 24 – Mean daily discharge at DWR Shackleford Creek gage – WY2005
cfs
100
90
Shackleford Creek - daily mean discharge WY2006
80
70
daily
mean
25 cfs
60
50
40
30
20
11/5/05
10
0
10/1/2005
↘
10/22/2005
11/12/2005
12/3/2005
date
12/24/2005
1/14/2006
Figure 25 - Mean daily discharge at DWR Shackleford Creek gage – WY2006
cfs
100
90
Shackleford Creek - daily mean discharge WY2007
80
70
60
50
daily
mean
40
30
11/12/06
↘
20
10
0
10/1/2006
10/22/2006
11/12/2006
12/3/2006
date
12/24/2006
1/14/2007
Figure 26 - Mean daily discharge at DWR Shackleford Creek gage – WY2007
XV
cfs
100
90
Shackleford Creek - daily mean discharge WY2008
80
70
60
11/13/07
↘
50
40
30
20
daily
mean
10
0
10/1/2007
10/22/2007
11/12/2007
12/3/2007
date
12/24/2007
1/14/2008
Figure 27 - Mean daily discharge at DWR Shackleford Creek gage – WY2008
In WY 2008 (Figure 27), Shackleford Creek became connected following the first significant
precipitation event in Mid- October 2007 but subsequently disconnected when the flows receded.
This pattern of intermittent connectivity was also observed in the early fall of 2008 (Table 2). In
the drought year of 2009, Shackleford Creek did not achieve connectivity until December 21st
and was observed disconnected the subsequent week. Connectivity did not return until January
1st, 2010. Analysis of the USGS data for this period shows the Scott River discharge exceeding
100 cfs on Dec. 21 and receding below 80 cfs on Dec. 28th. It is hypothesized that Shackleford
Creek attains connectivity when the USGS gage is in excess of 80-100 cfs.
cfs
USGS - Scott River below Fort Jones
WY2010 - provisional data
150
140
130
120
110
100
90
80
70
60
50
40
30
20
10
0
10/1/2009
daily mean cfs
10/22/2009
11/12/2009
12/3/2009
12/24/2009
date
Figure 28 – USGS daily mean discharge- data provisional – 10/1/09 – 1/1/10
Inspection of the flows at the Shackleford and USGS gages during WY2008 (Figure 29)
corroborates the observations of WY2010. Shackleford Creek’s discharge is less than 25 cfs in
approximately the same period that the USGS’s discharge is less than 100 cfs. These
observations lead to the hypothesis that Shackleford Creek achieves and maintains connectivity
when the Scott River at the USGS gage is greater than approximately 100 cfs. A significant
storm event connected Shackleford Creek during the drought year of 2001 on November 22nd
with no subsequent lack of connectivity. The observation made in December 2009 documented
the latest reconnection of Shackleford Creek during the nine year period of this report.
XVI
Shackleford Cr (DWR) and Scott River (USGS)
daily mean discharge - WY2008
cfs
140
120
100
Shackleford
25 cfs
USGS
80
60
40
20
0
10/1/2007
10/15/2007
10/29/2007
11/12/2007
11/26/2007
date
Figure 29 – Discharge at USGS and Shackleford gages – WY2008
Kidder Creek, Big Slough, Patterson and Johnson Creeks –
The west side tributaries between Etna Creek and Shackleford Creek are connected to the Scott
River at the confluence of Kidder Creek. Big Slough is created by the confluence of Johnson,
Crystal and Patterson Creek and Big Slough joins Kidder Creek north east of the town of
Greenview. Adult coho have been documented spawning and rearing in Kidder Creek and
Patterson Creek and are suspected to utilize portions of Johnson Creek for spawning and/or
rearing. This system of tributaries has significant reaches along the valley floor that are dry
during the average low flow period of late summer and early fall.
Past observations of connectivity demonstrate that connectivity is usually attained at the same
time in all of the streams following a significant precipitation event. For several years (2001,
2004, 2005, 2007) connectivity of Kidder and Patterson Creek follows the same event that
generated connectivity in Shackleford Creek. Observations in 2009 corroborate this for Kidder
Creek but document Patterson Creek achieving full connectivity almost 10 days later then Kidder
Creek. In the winter of 2008-2009, Patterson Creek was observed to be disconnected for periods
through February. The intermittent connectivity observed in the valley reach of Patterson Creek
during the winter months of low flow water years should be considered when evaluating the
desirability of introducing spawning habitat.
cfs
300
USGS - Scott River below Fort Jones
WY2009
250
200
150
100
daily mean cfs
50
0
10/1/2008 10/29/2008 11/26/2008 12/24/2008 1/21/2009
2/18/2009
date
Figure 30 – Mean daily discharge at the USGS – 10/1/08 – 2/22/09
Etna Creek –
XVII
Etna Creek is disconnected during the average low flow year from above Highway 3 to the
confluence with the Scott River. The observed connectivity of Etna Creek coincides closely to
the connectivity observed for Shackleford and Kidder Creek. Etna Creek achieved connectivity
on Dec. 21st, 2009 the same day as Shackleford Creek became connected and a day before
Kidder Creek was observed to be completely connected.
French Creek –
French Creek becomes disconnected for a short alluvial section in the lowest ½ mile before the
confluence with the Scott River during drier than average water years. French Creek has been
observed to be connected during average water years but the flow is probably not sufficient to
allow volitional passage of Chinook or coho salmon. The Cal. Dept. of Water Resources has
operated a stream discharge gage above the HWY3 Bridge since 2004. This location is
approximately 1 mile from the confluence with the Scott River. DWR has estimated that it takes
approximately 5 cfs of water at the gage to insure connectivity to the Scott River and 10 cfs of
water to insure volitional fish passage. For this analysis, the certified flow data from WY2005 –
WY2008 (Figure 31 – 34) will be reviewed with the 10 cfs criteria as the threshold for volitional
fish passage for adult salmon. The 10 cfs criteria was exceeded in mid October – Early
November for all of the water years displayed (10/23/04, 11/3/05, 11/3/06 and 10/16/07) and
flows in excess of 10 cfs are maintained after the initial data for all displayed water years except
WY2005. No connectivity issue was observed in WY2005.
cfs
100
French Creek - daily mean discharge
WY2005
80
60
mean daily cfs
10 cfs
40
20
0
10/1/2004 10/21/2004 11/10/2004 11/30/2004 12/20/2004
1/9/2005
date
Figure 31 – Daily mean discharge at French Creek gage – WY2005
cfs
100
French Creek - daily mean discharge
WY2006
80
60
40
mean daily cfs
10 cfs
20
0
10/1/2005 10/21/2005 11/10/2005 11/30/2005 12/20/2005 1/9/2006
date
Figure 32 - Daily mean discharge at French Creek gage – WY2006
XVIII
cfs
100
French Creek - daily mean discharge
WY2007
80
60
40
mean daily cfs
10 cfs
20
0
10/1/2006 10/21/2006 11/10/2006 11/30/2006 12/20/2006 1/9/2007
date
Figure 33 - Daily mean discharge at French Creek gage – WY2007
cfs
100
90
80
70
60
50
40
30
20
10
0
French Creek - daily mean discharge
WY2008
mean daily cfs
10 cfs
10/1/2007 10/21/2007 11/10/2007 11/30/2007 12/20/2007
1/9/2008
date
Figure 34 - Daily mean discharge at French Creek gage – WY2008
Analysis of the mean daily discharge at the USGS gage in the period in which French Creek
exceeded 10 cfs of discharge at the DWR gage shows that approximately 80 cfs is observed at
the USGS gage when the threshold criteria is met in French Creek (USGS - 10/23 – 10/24/04 60100 cfs, 11/3 – 11/4/05 – 60 cfs, 11/3 -4/06 – 80 cfs & 10/27 – 11/2/07 – 80 -100 cfs after run off
event). Chinook salmon have been observed spawning in lower French Creek in limited numbers
and there has never been a concern that coho salmon are unable to volitional enter French Creek
due to flow issues during the period of this report.
Moffett Creek–
Analysis of the mean daily discharge at the USGS gage in the period in which French Creek
exceeded 10 cfs of discharge at the DWR gage shows that approximately 80 cfs is observed at
the USGS gage when the threshold criteria is met in French Creek (USGS - 10/23 – 10/24/04 60100 cfs, 11/3 – 11/4/05 – 60 cfs, 11/3 -4/06 – 80 cfs & 10/27 – 11/2/07 – 80 -100 cfs after run off
event). Chinook salmon have been observed spawning in lower French Creek in limited
numbers, and there no known reports of coho salmon being unable to volitionally enter French
Creek due to low flows or the absence of surface flows during the period of this report.
Indian Creek –
Indian Creek has achieved connectivity to the Scott River two times during the period of this
report – December 27th, 2002 and after December 16th, 2005. It is important to note that Indian
Creek did not achieve connectivity in January 2002 when Moffett Creek became connected.
These observations lead to the conclusion that Indian Creek requires flows well in excess of
3,000 cfs in order to achieve connectivity.
XIX
cfs
3000
USGS - Scott River below Fort Jones
WY2002
2500
2000
1500
daily mean cfs
1000
500
0
10/1/2001
10/22/2001 11/12/2001
12/3/2001
12/24/2001
1/14/2002
date
Figure 35 - Mean daily discharge at the USGS – 10/1/01 – 1/15/02
cfs
3000
USGS - Scott River below Fort Jones
WY2005
2500
2000
daily mean cfs
1500
1000
500
0
10/1/2004
10/29/2004
11/26/2004
12/24/2004
1/21/2005
date
Figure 36 - Mean daily discharge at the USGS – 10/1/04 – 1/31/05
Two factors are hypothesized to limit the connectivity of Moffett and Indian Creek until a
significant persistent precipitation event generates flows in the Scott River in excess of 3,000 cfs:
1) legacy land use that has significantly altered the channel structure and watershed landscape,
and 2) both watersheds are in areas of relatively low precipitation (Map 2). Moffett Creek has
been observed to be intermittent throughout its low gradient valley reaches through the winter
months and the headwaters of the watershed are of lower elevation than the west and south side
of the Scott River limiting the amount of snow pack and the associated spring runoff.
Groundwater’s role in the connectivity of Moffett and Indian Creeks is largely unknown.
XX
Map 2 – Precipitation in Scott River Watershed
Conclusion –
This report details observations of main stem and tributary connectivity in relation to measured
discharge at the Scott River USGS gage and the DWR gages in Shackleford and French Creek. It
XXI
should be noted that the criteria of connectivity used in this analysis was connectivity with
discharge of a sufficient magnitude to allow migration of adult Chinook or coho salmon to a
reach above the location. This analysis has found three groupings of connectivity (Table 4). All
reaches of the Scott River and the East and South Fork become accessible when flows are in
excess of approximately 40 cfs at the USGS gage. The major west side tributaries become
accessible when discharge at the USGS gage is in excess of 80-100 cfs. The tributaries draining
the relatively dry watershed located in the north east need discharges in excess of several
thousand cfs at the USGS gage to become connected.
Access to (above)
Flow regime at USGS gage
Scott River - Scott Valley
30-35 cfs
Scott River - Above Tailing Pile
30-40 cfs
French Creek
80 cfs
Shackleford Creek
100 cfs
Kidder Creek
100 cfs
Patterson Creek
100 - 200 cfs
Moffett Creek
3,000 cfs
Indian Creek
5,000 cfs
Table 4 – Approximate flow regime observed at USGS gage when listed locations achieve
connectivity
Two major observations are generated by this analysis. 1) There is not a significant difference
between the magnitude of discharge needed to allow migration to the west side tributaries but
Moffett and Indian Creek need an order of magnitude greater flow to become connected and 2)
channel restoration should be considered as a potential for restoring connectivity at a lower
discharge threshold in key tributaries with short reaches of disconnection (e.g. Shackleford
Creek).
References:
Cal. Dept. of Water Resources (2010) accessed at http://www.water.ca.gov/waterdatalibrary/
Maurer, Sue. (2002) Scott River Watershed Adult Coho Spawning Survey December 2001January 2002. USDA, Forest Service Klamath National Forest. pp.122
Maurer, Sue. (2003) Scott River Watershed Adult Coho Spawning Survey December 2002January 2003. Siskiyou RCD pp. 130
Quigley D. (2004) Scott River Coho Spawning Assessment – 2003/2004 Season. Siskiyou RCD
pp. 27
Quigley, D.(2005) Scott River Watershed Adult Coho Spawning Ground Surveys 2004/2005
Season. Siskiyou RCD. pp 148.
Quigley, D.(2006) Scott River Watershed Adult Coho Spawning Ground Surveys 2005/2006
Season. Siskiyou RCD. pp 51.
Quigley, D.(2007) Scott River Watershed Adult Coho Spawning Ground Surveys 2006/2007
Season. Siskiyou RCD. pp 24.
USGS
–
National
Water
Information
System
(2010)
accessed
at
http://waterdata.usgs.gov/ca/nwis/rt
XXII