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An Evaluation of the Anadromous Fish Interim Instream Flow Need for the Lower Scott River, in Siskiyou County, California
Phase I
Final Report
Prepared for: Yurok Tribe
Prepared by:
Dr. Thomas B. Hardy Mr. Thomas A. Shaw
Watershed Systems Group, INC San Marcos, Texas 78666
August 3, 2015
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Executive Summary This report reviews the historical and existing status of flows as well as the periodicities of salmonids within the Scott River, California and highlights factors, which have been attributed to the decline in these fisheries. The report also makes interim flow recommendations for the Scott River necessary for the maintenance of base populations of these species. These interim recommendations are based on a variety of hydrology based modeling approaches that represent different, yet valid approaches to estimating required flow regimes in the absence of site specific data. The recommended interim flows seek to provide the basis or starting point upon which the existing California Department of Fish and Wildlife instream flow studies can build. Purpose of Report The purpose of this report is to provide an interim flow recommendation for flows through the canyon section of the Scott River sufficient for passage and rearing of adult and juvenile Chinook, and Coho Salmon and Steelhead Trout. Flows are affected by human influenced factors such as surface and groundwater withdrawals, as well as climactic effects such as droughts and low snowpack levels. This report does not make management recommendations for the provision of sufficient flow, but rather provides information as to what flows are necessary for the maintenance of salmonid populations in the Scott River. Acknowledgments The authors of this report respectfully acknowledge the work and accomplishments of the resources agencies, tribes, federal and private landowners, county, state, and private coordination groups, and the respective individuals for their diligent and relentless effort to preserve and protect the open range and dependent fish, wildlife, plants, and their habitat resources of the Scott River watershed.
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Table of Contents Executive Summary ............................................................................................................ 2 Purpose of Report ............................................................................................................... 2 Acknowledgments............................................................................................................... 2 List of Tables ...................................................................................................................... 4 List of Figures ..................................................................................................................... 5 Basin Description ................................................................................................................ 7 Adult Salmon Migration ..................................................................................................... 8
Redd Scour Potential..................................................................................................... 12 Coho Salmon Adult Migration.......................................................................................... 14 Spawning........................................................................................................................... 16 Embryos and Juveniles ..................................................................................................... 18 Instream Flows .................................................................................................................. 20
Water Year Classifications for the Scott River ............................................................. 21 Assessment of Interim Flow Needs .............................................................................. 23
Hoppe Method .......................................................................................................... 23 New England Flow Recommendation Policy ........................................................... 24 Northern Great Plains Resource Program Method ................................................... 25 Tennant Method ........................................................................................................ 26 Washington Base Flow Method: ............................................................................... 28
Hydraulic Analysis: ...................................................................................................... 29 Combined Passage Estimates ........................................................................................ 32
California Department of Fish and Wildlife Recommended Interim Instream Flows...... 33 Passage .......................................................................................................................... 33 Spawning and Juvenile Rearing .................................................................................... 33 CDFG Recommended Interim Minimum Instream Flow ............................................. 33
Summary and Conclusions ............................................................................................... 35 References ......................................................................................................................... 38
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List of Tables Table 1. Scott River salmonid species and development stage periodicities. .................. 20 Table 2. Water year types and associated mean annual flow range comparisons (cfs) between the Period of Record (1942-2012), Historical (1942-1971), and Present (1983-2012) periods. ................................................................................................................... 22 Table 3. Period of Record (1942-2012), Historical (1942-1971), and Present (1983-2012) mean monthly flow (MMF), percent of MAF, and percent of MAF for an average water year (50% exceedance). .................................................................................................... 23 Table 4. Historical flows for associated monthly exceedance values used in various hydrology methods derived from an analysis of the daily flow records from the USGS stream gauge 11519500 (SCOTT R NR FORT JONES CA) for water years 1942-1971.23 Table 5. Estimated monthly instream flows for the Scott River USGS gauge near Fort Jones, CA based on application of the Hoppe Method. .................................................... 24 Table 6. Estimated monthly instream flows based on application of the New England Aquatic Base Flow Method. ............................................................................................. 25 Table 7. Estimated monthly instream flows based on application of the Northern Great Plains Resource Program Methodology............................................................................ 26 Table 8. Instream Flow Regimes for Fish, Wildlife, Recreation and Related Environmental Resources Recommended Base Flow Regimes (% Mean Annual Flow). 27 Table 9. Estimated monthly instream flows based on application of the Tennant using the mid-point of the Optimum Range or 0.8 of the MAF. ...................................................... 28 Table 10. Estimated monthly instream flows based on application of the Washington Base Flow Method. ........................................................................................................... 29 Table 11. Example calibration results for WinxsPro. ...................................................... 31 Table 12. Averaged instream flow methods and the Minimum Instream Flow Recommendation (MIFR) in cfs and MIFR and the USFS for the Scott River Canyon. . 32 Table 13. The CDFW recommended minimum, interim instream flows for the Scott River at the USGS streamflow gauge 11519500 near Fort Jones, CA. ............................ 34
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List of Figures Figure 1. Scott River Basin maps including: location, relief, geomorphic units and channel types, and average precipitation (Quigley et al., 2001). ........................................ 7 Figure 2. Scott River adult Fall Chinook salmon spawning escapement numbers (1978-2010) and percent of the Klamath Basin’s natural escapement (non-hatchery). ................ 9 Figure 3. Biweekly percent of the annual Fall Chinook salmon run passing through the Lower Klamath River (1981–1992). ................................................................................. 10 Figure 4. Adult fall Chinook salmon timing expressed as biweekly, average percent of annual totals for the Shasta River, Scott River, Bogus Creek and Iron Gate Hatchery (1980-1986)....................................................................................................................... 10 Figure 5. Scott River Fall Chinook average percentage of annual totals from CDFW lower Scott River Canyon weir (rkm 2.6, 1989-1991) and upper Scott River Canyon weir (rkm 29.3, 2007-2012). ..................................................................................................... 11 Figure 6. Over 300 adult Fall Chinook holding in the Highway 96 bridge pool near the mouth of the Scott River (photo by Michael Hupp, September 30, 2012). ...................... 12 Figure 7. Daily passage of Fall Chinook salmon through the Scott River, CDFW counting station located near the top of the Scott River lower canyon (rkm 29.3), and Scott River discharge measured at the USGS gauging station near Fort Jones, CA (rkm 33.0). ................................................................................................................................. 13 Figure 8. Number and percentage of Fall Chinook spawning below and above the CDFG counting facility (rkm 29.3) for the years 2008-3012 (Knechtle 2013 pers. comm.). ...... 13 Figure 9. Scott River Fall Chinook spawning distribution, Scott River Canyon reach to rkm 35.2 (left) and Scott River Valley reach to Fay Lane rkm 79.3 (right). .................... 14 Figure 10. Biweekly percent of the annual Coho salmon run passing through the Lower Klamath River (1981–1988). ............................................................................................ 15 Figure 11. Adult Coho timing expressed as biweekly, average percent of annual totals for the Shasta River, Scott River, Bogus Creek and Iron Gate Hatchery (1981-1995). ......... 15 Figure 12. Daily passage of Coho salmon through the Scott River, CDFW counting station located near the top of the Scott River lower canyon (rkm 29.3), and Scott River discharge measured at the USGS gauging station near Fort Jones, CA (rkm 33.0, CDFW data)................................................................................................................................... 16 Figure 13. The relationship between flow and usable spawning habitat, demarking minimal and optimal flows (Thompson 1972). ................................................................ 17 Figure 14. Scott River juvenile Chinook, Coho, and outmigration timing (mean percent) for the CDFW juvenile salmonid trapping facility. .......................................................... 19 Figure 15. Scott River historical (1942-1971) and present (1983-2012) biweekly percent exceedance for the months September through November. Data summarized from the USGS gauging station (11519500), near Fort Jones CA records. .................................... 21 Figure 16. Mean annual flow duration for the Scott River at Fort Jones for the Period of Record (1942-2012), Historical (1942-1971), and Present (1983-2012) periods. ............ 22 Figure 17. Survey transects were located on the Scott River at rkm 11.0, approximately 0.75 rkm upstream of McGuffy Creek. ............................................................................. 30 Figure 18. Study site transect locations for collection of discharge and cross section geometry data. ................................................................................................................... 30 Figure 19. Scott River geometry and water surface elevation at 105 cfs. ....................... 31
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Figure 20. Normalized percent of passage area as a function of discharge (cfs). ............ 32 Figure 21 Comparison between CDFW, MIFR, USFS Instream flow recommendations, and mean monthly flow for the period 1942-1971, for the periods September-October and November-December. ................................................................ 34 Figure 22. Scott River juvenile Chinook production estimates for years 2000-2006 (Chesney et al., 2007). ...................................................................................................... 36 Figure 23. U.S. Geological Survey time-series daily discharge for the Scott River near Fort Jones, CA. Site: 11519500 September 1 – December 31, 2005, logarithmic scale. . 36 Figure 24. Average daily water temperature measured at the mouth of the Scott River and daily counts of adult Fall Chinook enumerated at the CDFW weir (rkm 29.3) during the fall of 2008. ................................................................................................................. 37 Figure 25. Scott River discharge measured at USGS Scott River near Fort Jones, CA. and daily counts of adult Fall Chinook enumerated at the CDFW weir (rkm 29.3) during the fall of 2008. ................................................................................................................. 37
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Basin Description The Scott River basin is rectangular in shape, measuring approximately 2,121square kilometers (kms), The basin has general dimensions of 64 kms, from the north to south, and 34 kms, from east to west (Mack 1958). The watershed is located within the Klamath Mountains of Siskiyou County, in northern California (North Coast Regional Water Quality Control Board 2005). The Scott River generally flows northward entering the Klamath River at river kilometer (rkm) 230. The basin is approximately two-thirds privately owned and one-third publicly owned. Approximately, 45 percent of the land is managed for forestry, 40 percent grazing, and 13 percent as cropland. The remaining 2 percent is used for various other purposes (Quigley et al. 2001, Figure 1).
Figure 1. Scott River Basin maps including: location, relief, geomorphic units and
channel types, and average precipitation (Quigley et al., 2001).
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The Scott River is an important contributor to the anadromous resources of the Klamath River. However, the Scott River fishery resources have experienced dramatic declines attributed to habitat degradation, from the diversion of water and excessive sediment entering the stream channel (CDWR 1991). During July through October, there is only limited streamflow available for the fishery, with irrigation demands often exceeding available surface flows (CDWR 1991). Adult Salmon Migration Adult salmon migrate from the Pacific Ocean through the entrance of the Klamath River on their spawning migration, using their olfactory memory to navigate back to the natal areas where they were born. As they enter into the freshwater environment, feeding ceases and their metabolic energy is now a finite resource of lipids and proteins used to fuel their upstream migration, mature gonads, spawn, and defend redd sites. Pacific salmon utilize up to 50% of their stored energy during migration, with extended or delayed migration being a source of premature mortality, primarily due to energy exhaustion (Hasler et al. 2012). The adults evolved adaptations to their swimming strategies, migratory timing and behaviors, and the use of habitat that conserve their limited energy supply. The migrating adults will select energy efficient upstream pathways in order to reduce expenditures by seeking areas of low opposing velocities, metabolically optimal temperatures, and swimming behaviors (burst and sustained) resulting in an optimal migration rate. Metabolic costs increase when the adults migrate through constricted reaches with rapids and islands, in comparison to pool reaches (Hasler et al. 2012, Hinch 2006). Strange (2012) found adult Chinook migration through the Lower Klamath River was inhibited at lower mean daily river temperatures during periods of increasing river temperatures, than periods of declining temperatures. The ability of Chinook to correctly determine the onset of declining or inclining river temperature is a vital mechanism for taking advantage of brief thermal migratory windows (Strange 2012). The timing of this spawning migration is imperative having successfully evolved over a multitude of generations favoring the adult’s ability to successfully reach their natal spawning grounds. Reproductive costs are greater for females than males of similar fork-lengths. Comparisons with successful spawners from the South Fork Salmon River in Idaho, researchers found males weighing 11% less and females weighing 45% less than fish near the start of migration. Males of mean fork length (82.5 cm) used 77% of their initial somatic energy stores to migrate and spawn while females of mean fork length (82 cm) used 87%. From the time the Chinook passed Bonneville Dam to death, these fish, depending on gender, used 97-99% of their muscle and 76-81% of their visceral lipid stores. However, an excessive use of energy due to various complications associated passage during their upstream migration can result in reduced spawning success, loss of egg production, or increased pre-spawning mortality (Mesa and Magie 2004).
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The Scott River is a significant Fall Chinook spawning tributary to the Klamath Basin. During the 1996-98 return years, an average of 30.6% of the total natural Fall Chinook natural escapement for the Klamath Basin above the Trinity River confluence entered the Scott River. Since 1978, the number of Scott River returning adult Chinook has ranged from a high of 14,477 fish to low of 467 and on average represents approximately 10% of the Klamath Basin’s natural escapement (Knechtle and Chesney 2010, Figure 2).
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Figure 2. Scott River adult Fall Chinook salmon spawning escapement numbers (1978-
2010) and percent of the Klamath Basin’s natural escapement (non-hatchery). Fall Chinook begin their entry into the Klamath River during mid-July. The run peaks in the Lower Klamath River during early September, then tails off by the end of October (Figure 3). A smaller run of Late Fall Chinook follows the Fall Chinook through December (Hardy et al., 2006, Shaw et al., 1997). Chinook typically reach their spawning tributaries 2 to 4 weeks after freshwater entry (NRC 2004). Snyder (1931) reported that in certain cases, the timing of arrival of salmon to the tributaries differed markedly and their degree of maturity also varied. Shasta River Chinook run appears to peaks about two weeks earlier (October 1-15) than the Scott River (October 15-31), but numbers of Chinook entering the Shasta River extend well into the October 15-31 period, with the Scott River Chinook extending well into early November (Figure 4). “During the week beginning October 16, 1927, a relatively small number of the fish held between the Klamathon Racks were ripe, while in Shasta River a large numbers were actively spawning, with many spent and a few dead fish being observed. At the same time, only a few fish were in Scott River, with the migration having scarcely begun. Spawning had not yet started in the Scott while the volume of Scott River, at the time, was equal to or greater than that of the Shasta (Snyder1931).”
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Figure 3. Biweekly percent of the annual Fall Chinook salmon run passing through the
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Figure 4. Adult fall Chinook salmon timing expressed as biweekly, average percent of
annual totals for the Shasta River, Scott River, Bogus Creek and Iron Gate Hatchery (1980-1986).
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The California Department of Fish and Wildlife (CDFW) operates a fish counting facility (weir) on the mainstem Scott River to assess the annual Chinook and Coho escapement and run characteristics. During the period 1989-1991, the weir was located at rkm 2.6, near the mouth of the Scott River. The weir was discontinued for 16 years, and then reinstated at rkm 29.3, near the top of the Canyon reach (rkm 0–35.2). Adult Chinook ascend 230 rkms of the Klamath River before entering the Scott River in early-September. The run peaks in mid-0ctober and ends in early December (Hardy et al., 2006, Shaw et al., 1997, and CDFW 2010). A comparison between the passage of adult Chinook through the historical Scott River weir site located at rkm 2.6 and the present weir location, at rkm 29.3, give a cursory view of the adult Chinook migration timing through the lower Scott River Canyon reach (Figure 5). During low flow conditions, the Scott River adult Fall Chinook may delay their ascent upriver, concentrating in the lower canyon reach, by both holding in pools (Figure 6) and spawning (Quiñones 2005, SRWC 2005). When conditions are favorable, the adult Chinook begin their migration through the lower Scott River (rkm 2.6) beginning in early September, peaking during mid-October, and typically concluding in late-November. During some years, a late run of Fall Chinook continue entering the Scott into mid-December. When conditions provide unrestricted passage, adult movement through the present weir location, at rkm 29.3 begins in late-September, peaks during the last three weeks of October, and concludes by late-November (Figures 5 and 7). Clayton (2006) reported that in the early November 2005 discharge at Fort Jones peaked at 488 cfs, and gave the Fall Chinook access to spawning areas in the valley reaches, Shackleford Creek, and the East and South Forks of the Scott River.
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Figure 5. Scott River Fall Chinook average percentage of annual totals from CDFW lower Scott River Canyon weir (rkm 2.6, 1989-1991) and upper Scott River Canyon weir (rkm 29.3, 2007-2012).
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Figure 6. Over 300 adult Fall Chinook holding in the Highway 96 bridge pool near the
mouth of the Scott River (photo by Michael Hupp, September 30, 2012). We examined the daily adult Fall Chinook run timing through CDFW fish counting facility (rkm 29.3) in conjunction to daily flows, along with the annual number and percentage of Chinook spawning above and below the counting facility. Based on our evaluation, there appears to be an effect from low flows on the adult run timing through the Canyon reach. The adult Chinook passing the counting station were either absent or delayed during the early season. The percentage of Chinook spawning in the Canyon reach below the weir also appears to increase during low flow periods, and to a greater extent, during years with lower escapement (Figure 8).
Redd Scour Potential The lower Canyon reach is a higher gradient, confined channel, with narrow valley walls. Overbank flows have a limited floodplain resulting in increased depths and velocities in the active channel where Chinook salmon spawn. During peak flow events there is a much higher redd scour potential, in comparison with the Valley reach that has a lower gradient, less confinement, higher sinuosity, and a larger floodplain (Figure 9). Given volitional passage, adult salmonids have over 80 rkms of habitat and were observed well above Fay Lane (rkm 79.3), and the lower portions of the larger Scott River tributaries (Yokel 2008).
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Figure 7. Daily passage of Fall Chinook salmon through the Scott River, CDFW counting station located near the top of the Scott River lower canyon (rkm 29.3), and Scott River discharge measured at the USGS gauging station near Fort Jones, CA (rkm 33.0).
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counting facility (rkm 29.3) for the years 2008-3012 (Knechtle 2013 pers. comm.).
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Figure 9. Scott River Fall Chinook spawning distribution, Scott River Canyon reach to
rkm 35.2 (left) and Scott River Valley reach to Fay Lane rkm 79.3 (right). Other evidence of restricted passage includes an observation on September 28, 2009 when CDFW conducted a reconnaissance survey on the lower Scott River, when flows at the USGS gauging station near Fort Jones were 7 cfs. Surveyors observed large numbers of adult Chinook salmon holding in pools below Scott Bar. Two dead adult Chinook were collected, with both fish infected with Columnaris and Ich (CDFG 2009). Quiñones (2005) reported that the Scott River Chinook salmon spawning distribution is dependent on flows, with the valley having the highest concentrations of spawning in years of high flows and the canyon during years of low flows. Quiñones (2005) reported their 2004 survey found that most of the Chinook spawning was concentrated in the canyon due to low flows (20-120 cfs) throughout the survey period (Quiñones 2005). Coho Salmon Adult Migration Coho salmon adults begin their upstream migration through the Lower Klamath River in early September and peak in early to mid-October (Figure 10). They begin their entry into Iron Gate hatchery, Bogus Creek, Shasta River and Scott River in early October, peak in late October and early November, and tail off in mid to late December (Figure 11). Migrating adult Coho salmon were first observed migrating through the Scott River counting facility in mid-October, peaking in mid-November, and tailing off in late December (Figure 12). We examined the potential for low flow delays in the Scott River and observed possible flow related delays during 2009. The passage of the adult Coho run through the lower Canyon reach appeared to be delayed past the mid-November period, peaking in mid-December when flows reached approximately 80 cfs. During most years, the adult Coho migration is triggered by discharge increases (Figure 12).
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Figure 10. Biweekly percent of the annual Coho salmon run passing through the Lower
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Figure 11. Adult Coho timing expressed as biweekly, average percent of annual totals for
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Figure 12. Daily passage of Coho salmon through the Scott River, CDFW counting station located near the top of the Scott River lower canyon (rkm 29.3), and Scott River discharge measured at the USGS gauging station near Fort Jones, CA (rkm 33.0, CDFW data).
Spawning Adult salmonids that reach their spawning grounds and successfully spawn during the right time period and locations have an increased likelihood for successful embryo development. The young Chinook will emerge in time to feed and grow as they emigrate downstream, eventually entering the marine environment at the correct time and size (Quinn 2005). Streamflow regulates the amount and suitability of the spawning areas. As flow increases, salmonid spawning area becomes usable, rising with flow, and eventually
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reaching an optimal level of available spawning habitat. As flow continues to rise, water velocities exceed the suitable range for spawning in some areas while creating acceptable spawning habitats other areas. Eventually, the losses outweigh the gains, and amount of suitable spawning area decreases. When spawning area is plotted against streamflow, the curve will typically rise to plateau followed by a gradual decline (Figure 13).
Figure 13. The relationship between flow and usable spawning habitat, demarking minimal and optimal flows (Thompson 1972).
When flows exceed bank full, the rate at which flow depth and shear stress will increase to the point that flow velocities surpass the critical shear stress and the initiation of gravel movement occurs. Gravel movement within the spawning areas increasing the likelihood of redd scour, with high egg mortalities. The rate of increasing shear stress in the spawning channel is dependent upon the valley and floodplain geometry, with the Canyon reach being confined; with a higher redd scour potential, in comparison to the Valley reach. On the Middle Fork of the Salmon River in Idaho, Chinook were found to maintain a distribution within stream reaches that were skewed towards low critical scour probability (Goode et al., 2013). Alterations of the natural hydrograph can impede adult salmonid passage through the lower Scott River canyon reach, during periods when the historical Chinook had unimpeded passage into the spawning areas within the Scott River Valley reach and tributaries. The adults with impeded passage then spawn in the lower Canyon reach where they become vulnerable to high water velocities and associated bed scour, as well as, redd superimposition.
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Scott River Chinook salmon begin spawning in early October and typically conclude by the end of November (Knechtle and Chesney 2011). Adult Coho spawning begins in early October, continues in through December, and tapered off during January, 2002 (Maurer 2002). Embryos and Juveniles Salmonid embryos have survived dewatering of redds by obtaining oxygen from the air prior to hatching when suitable temperatures, lack of excessive fine sediment, and 100% humidity were present. When relative humidity was kept at 100%, Chinook embryos have survived dewatering for 24 hours, but all the embryos died when the humidity was lowered to 90% (Neitzel and Becker 1985). The required time to hatch and to emerge as alevins (0+) varies by species and perhaps by location. For example, time to 50% hatch for Pacific salmon species ranges from 115 to 150 d at 4°C and from 35 to 60 d at 12°C. Once incubation is complete and the alevins must emerge from the egg pocket, through the interstitial spaces of the streambed. Upon emergence from the gravel nests, the young-of-the-year (0+) salmon seek conditions that provide security from predators or other disturbances. Overhanging vegetation along shorelines and undercut banks serve as cover during high flow conditions, and at other times, the juveniles are found within one swimming burst of cover provided by overhanging banks, tree stumps and branches, and boulders. Bank irregularities provide small pools and current eddies, with little or no velocities for rearing juveniles. Juvenile chinook salmon are found to be closely associated to cover in the main channel and in places where the river braided and the water is shallow. Figure 14 displays the timing of 0+ Chinook, Coho and steelhead as they disperse downstream and are captured by the CDFW fish traps. The Chinook emergence and downstream movement begins in late February, peaking from late March through late April, as 0+ fry. The larger 0+ smolt Chinook outmigrate from early June through early July. Coho 0+ begin their fry dispersal in early April, peak in mid-April through early May. As with Chinook, there is a second peak movement of juvenile 0+ Coho in early June through early July. Steelhead 0+ begin their dispersal in early May, peaking in mid-June through early July (Figure 14). Both the Coho and steelhead require at least 18 months of freshwater rearing while the Chinook only requiring up to 6 months. Therefore, 0+ Coho and steelhead must complete their freshwater rearing phase in the upper and low Scott River, the Scott River tributaries, the Klamath River, or non-natal tributaries of the Scott and Klamath Rivers (Figure 14). The 1+ Coho were captured while passing the Scott River trapping location from mid-February through early July. The 1+ and 2+ steelhead were observed from mid-February through mid-June (Figure 14). Table 1 provides a summary of the Scott River salmonid species and primary development stages periodicities.
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Figure 14. Scott River juvenile Chinook, Coho, and outmigration timing (mean percent)
for the CDFW juvenile salmonid trapping facility.
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Table 1. Scott River salmonid species and development stage periodicities.
Species and DevelopmentChinook Adult Migration x x x x x x xChinook Spawning x x x xChinook 0+ Fry x x x x x xChinook 0+ Juvenile x x x x xCoho Adult Migration x x x x x xCoho Spawning x x xCoho 0+ Fry x x xCoho 0+ Juvenile x x x x x x x x x x x x x x xCoho 1+ Juvenile x x x x x x x x x x x xSteelhead Adult Migration x x x x x x x x xSteelhead Spawning x x x x x x xSteelhead 0+ Fry x x x xSteelhead 0+ Juvenile x x x x x x x x x x x x xSteelhead 1+ and 2+ Juvenile x x x x x x x x x x x x x x x x x x x x x x x x
DecJul Aug Sep Oct NovJan Feb Mar Apr May Jun
Instream Flows The Scott River basin supports large agricultural areas, with approximately 46 square miles (120 square kilometers) utilized for the grazing along with the production of alfalfa and grain Van Kirk and Naman (2008). Altered instream flows can be an issue for holding, migration, spawning, egg incubation, rearing, and downstream migration of anadromous fish. West et al. (1990) reported that poor summer flows that influence the quantity of habitat available for rearing purposes were a result of heavy water withdrawal on agricultural land. The authors recommended augmenting flows or the regulation of water withdrawals to provide summer rearing habitat and Chinook spawning migration access. Instream flows in the Scott River and tributaries can be low from late June through November. Tributaries with large alluvial fans can become subsurface and disconnected from the Scott River during average to dry years, primarily due a high rate of seepage into the alluvial fans and diversions for irrigation (NRC 2004). During August and September and into the fall, Scott River surface flows also become disconnected during average and dry years. In average and wet years, the continuity of flow occurs during late October and early November as evapotranspiration declines and irrigation decreases (NRC 2004). In dry years, low-flow conditions persist until substantial rainfall occurs. The low summer and early fall base flow is a natural characteristic of the hydrograph. However, water management has increased the frequency and duration of negligible flow (NRC 2004). According to Van Kirk and Naman (2008), late-summer base flows in the Scott River have significantly declined in comparison to other Klamath River subbasins (Trinity River, Salmon River, Indian Creek, and the South Fork Trinity River). Daily flows from July 1 through October 22 showed a large decrease in means in comparison to the historical period, with an estimated decline of 61%, due to local factors. An approximated 21 cfs of the 37 cfs late summer decline was attributed to watershed
21
factors, including consumptive use, with the remaining 39% of the late summer decline was attributed to regional scale climatic factors We compared the percent exceedance for the biweekly periods, September through November over the two periods of record, historical (1942-1971) and present (1983-2012). Large deviations between the two periods were observed (Figure 15)
0102030405060708090
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November 16-30 Historical November 16-30 Present Figure 15. Scott River historical (1942-1971) and present (1983-2012) biweekly percent
exceedance for the months September through November. Data summarized from the USGS gauging station (11519500), near Fort Jones CA records.
Water Year Classifications for the Scott River Monthly flows indicative of five water year classifications were estimated from USGS gage data. These flows were used for comparative purposes of what different types of water year flow patterns may have looked like under “Historical” conditions compared to existing conditions. We define “Historical” conditions as flow prior to 1971 versus “Present” conditions represented by post 1971 hydrology. The choice of 1971 to split the
22
hydrologic record was somewhat arbitrary but based on the fact that rapid development of water resources in terms of agriculture deliveries are substantially higher in the post-1971 period (NRC 2004). These water year classifications were based on the same exceedance ranges of mean annual flow as utilized in the ‘Trinity River Flow Evaluation Study’ (USFWS 1999). Specifically, the mean annual flow for each water year at the Scott River at Fort Jones gage for the Period of Record (1942-2012), Historical (1942-1971), and Present (1983-2012) periods were used to compute the corresponding mean annual flow duration curve (see Figure 16). Water year classifications were associated with the following exceedance ranges: extremely wet (< 12 percent); wet (> 12 percent and < 40 percent); normal (> 40 percent and < 60 percent); dry (> 60 percent and < 88 percent); and critically dry (> 88 percent). The average of all mean annual flows which fell into a particular water year classification category was then assigned as the mean annual flow for that water year category as listed in Table 1. The mean annual flow for each water year category was then partitioned into monthly values utilizing the percent of mean annual flow based on the three time periods (Table 2).
0
200
400
600
800
1,000
1,200
1,400
1,600
0 10 20 30 40 50 60 70 80 90 100
Percent of time equalled or exceeded
Mea
n an
nual
flow
(cfs
)
Period of record Historical (1942-1971) Present (1983-2012) Figure 16. Mean annual flow duration for the Scott River at Fort Jones for the Period of
Record (1942-2012), Historical (1942-1971), and Present (1983-2012) periods.
Table 2. Water year types and associated mean annual flow range comparisons (cfs)
between the Period of Record (1942-2012), Historical (1942-1971), and Present (1983-2012) periods.
Extremely Wet Wet Normal Dry Critically Dry(< 12 percent) (>12 and <40) (>40 and < 60) (>60 and < 88) (> 88 percent)
Period of Record 0 1,040 - 710 710 - 444 444 - 276 276Historical 0 1,080 - 754 754 - 481 481 - 365 365Present 0 978 - 647 647 - 429 429 - 193 193
23
Assessment of Interim Flow Needs The Historical flow records were used to derive monthly flow exceedance values for use in several hydrology based methods for deriving instream flow recommendations (Table 3 and 4). Table 3. Period of Record (1942-2012), Historical (1942-1971), and Present (1983-2012)
mean monthly flow (MMF), percent of MAF, and percent of MAF for an average water year (50% exceedance).
January 1,050 198.6 166.7 1,118 175.9 167.8 917 192.5 157.9February 1,096 207.3 174.0 1,250 196.6 187.6 958 201.0 164.9March 1,022 193.4 162.3 885 139.2 132.8 1,092 229.2 188.0April 1,022 193.3 162.3 1,080 170.0 162.2 1,003 210.6 172.7May 1,154 218.4 183.3 1,235 194.2 185.3 1,106 232.1 190.4June 722 136.7 114.7 771 121.2 115.7 691 145.1 119.0July 185 35.0 29.4 202 31.8 30.3 174 36.6 30.0August 59 11.2 9.4 77 12.2 11.6 43 9.0 7.4September 49 9.4 7.8 62 9.8 9.3 36 7.5 6.1October 101 19.1 16.0 140 22.1 21.0 64 13.5 11.1November 306 57.9 48.6 332 52.2 49.8 233 49.0 40.2December 790 149.5 125.5 843 132.6 126.5 625 131.2 107.6
Percent of MAF
Percent of MAF (50% Exceedance)
Percent of MAF
Percent of MAF
Percent of AF (50% Exceedance)
Historical MMF cfs (1942-1971)
Period of Record MMF cfs (1942-2012)Month
Percent of MAF (50% Exceedance)
Present MMF cfs (1983 - 2012)
Table 4. Historical flows for associated monthly exceedance values used in various
hydrology methods derived from an analysis of the daily flow records from the USGS stream gauge 11519500 (SCOTT R NR FORT JONES CA) for water years 1942-1971.
Exceedance Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep
5 338 1,190 2,940 3,740 4,000 1,930 2,148 2,550 1,765 583 151 10310 131 755 1,630 2,485 2,410 1,483 1,888 2,180 1,544 404 119 9115 108 509 1,208 1,900 1,865 1,278 1,700 1,900 1,356 317 104 8520 103 374 995 1,590 1,560 1,156 1,560 1,708 1,206 267 96 7625 94 313 825 1,245 1,415 1,056 1,415 1,535 1,055 228 90 7330 88 266 707 1,020 1,310 977 1,305 1,435 925 200 84 7035 86 236 591 844 1,207 895 1,211 1,326 805 179 81 6540 80 204 499 734 1,084 838 1,138 1,232 727 161 77 6245 78 173 426 648 990 804 1,064 1,156 679 147 73 5950 73 150 359 560 905 765 997 1,071 619 136 70 5755 67 142 315 484 800 722 906 1,017 578 127 67 5560 63 127 270 397 710 678 824 955 538 119 63 5365 60 115 231 342 639 634 745 885 483 112 61 5170 57 108 198 296 544 580 631 815 441 103 59 4975 54 103 171 253 479 536 618 736 399 97 55 4780 52 91 158 203 379 494 571 663 347 90 51 4585 50 80 140 174 323 440 503 594 299 80 47 4290 46 65 119 160 268 368 418 530 259 71 44 4095 40 57 86 130 206 291 340 450 198 64 37 32
Hoppe Method This method was developed from studies on the Frying Pan River, Colorado and estimates flow requirements from percentiles on an annual flow duration curve for salmonid species. A flow that is equaled or exceeded 17 percent of the time is set for a
24
48 hour period to maintain flushing flows. As noted previously, this component of the flow regime is not addressed quantitatively in this report. The flow that is equaled or exceeded 40 percent of the time is recommended for protection of spawning flows and the flow that is equaled or exceeded 80 percent of the time is recommended to maintain flows for food production and aquatic cover. In essence, this approach strives to protect the higher flow component associated with the spring high flow spawning period and to provide survival habitat in terms of food production and physical habitat during the low flow periods. The biological rationale for this approach was adapted for the Scott River by using the monthly 40 percent exceedance flows to protect spawning and incubation for the September through February period, the monthly 60 percent exceedance flows during March through May period to protect incubating eggs and the monthly 80 percent exceedance flows for the June through August period for food production and protection of rearing habitats for fish. The actual monthly exceedance values were utilized in order to preserve the characteristics of the Historical flow patterns within a normal water year. The exceedance values for each monthly time period were derived from Table 4 and the resulting instream flows for each month utilizing this approach are provided in Table 5. Table 5. Estimated monthly instream flows for the Scott River USGS gauge near Fort
Jones, CA based on application of the Hoppe Method.
New England Flow Recommendation Policy This method is based on the assumption that aquatic resources have evolved to survive the most severe or adverse environmental conditions in the most stressful month of the year and encompasses both salmonid and invertebrate species. Utilizing hydrology records, the aquatic base flow is set as the median August flow, unless superseded by
25
spawning requirements which are equivalent to the historical median flow throughout the spawning period. Where inadequate flow records exist or where flows have been altered from water projects, recommendations are derived from the average median August flows computed from representative streams in the region in terms of cubic feet per square mile (cfsm). In this instance, the ‘default’ flows are 0.5 cfsm for all times of the year unless superseded by spawning and incubation flows which are defined as 1.0 cfsm in the fall/winter or 4.0 cfsm in the spring for the entire applicable spawning and incubation periods. This method was adopted for application in the Scott River by computing the flow associated with the 50 percent exceedance value for the spawning period from September to November using the daily flow records at Fort Jones for the 1942-1971 period of record. The computed flow was 78 cfs. A similar approach was taken for the incubation/emergence period during December through April using Fort Jones daily flow records for the 1942-1971 period of record. The computed flow at the 50 percent exceedance was 718 cfs. Finally, the daily gage data for August at Fort Jones using the daily flow records from the 1942-1971 period of record was computed as 70 cfs. The corresponding monthly values are provided in Table 6. Table 6. Estimated monthly instream flows based on application of the New England
Aquatic Base Flow Method.
Northern Great Plains Resource Program Method This method was developed from the assumption that established aquatic resource populations (independent of species composition) are a result of normal or average flows as opposed to ‘abnormal’ flows (e.g., extreme low or high flow components of the flow regime). The approach is based on the computation of mean monthly flows from the existing period of record and in the situation where the mean monthly flows are normally distributed, the ‘t’ statistic is used the establish the bounds for normal flows. That is, extreme values are discarded. Where mean monthly flows are not normally distributed, and then professional judgment is utilized to censor the data records. The daily flow
26
records for each retained month are then used to construct monthly flow duration curves and the flow that is equaled or exceeded 90 percent of the time is specified as the required flow to protect the aquatic ecosystem in that month. Further adjustments are made to recommended flows during the spring runoff period using a flow that is ‘near the mean annual flow of record’ during the high flow months. During low flow months, additional reductions in the flow may be made where ‘sharing’ of water with beneficial out of stream uses may be warranted. These two flow adjustments are based on professional judgment and negotiations. Adjustments for low flow months was deemed inappropriate given the status of the anadromous stocks in Scott River as noted previously, the high flow component is not considered under Phase I. The corresponding 90 percent exceedance values were then obtained from the monthly flow duration analyses. The corresponding recommended monthly flows are provided in Table 7. Table 7. Estimated monthly instream flows based on application of the Northern Great
Plains Resource Program Methodology.
Tennant Method This basic methodology attempts to protect the health of aquatic habitat based on an observed correlation between habitat conditions and flow regime as a percentage of the mean annual flow. The technique was developed from a variety of streams which were dominated by salmonid species but has been broadly applied to a wide range of systems including non-salmonid systems. Table 8 lists the criteria developed by Tennant for different levels of aquatic habitat protection. Tennant is broadly accepted in the literature as a reconnaissance-level technique. It was previously employed by Trihey (1996) to estimate instream flow requirements for tribal trust species in the Klamath River. These estimated flows subsequently served as a basis by which the ‘Modified Yurok’ flow regime proposal was developed for consideration in Klamath Project operations. The
27
modified Yurok proposal was developed through a facilitated workshop of Klamath Basin fisheries biologists and represents a DELPHI based recommendation. At its most fundamental level, the Tennant Method relies on the available long term gage data to derive an exceedance based flow level. As such, it inherently incorporates the range of water year variability by nature of the flow-exceedance basis of the computations. What remains difficult however is the selection of an ‘appropriate’ percent of the mean annual flow to utilize and how then this flow volume should be partitioned between various months based on the life history needs of the target species and life-stages. Table 8. Instream Flow Regimes for Fish, Wildlife, Recreation and Related
Environmental Resources Recommended Base Flow Regimes (% Mean Annual Flow).
There is no widely accepted ‘method’ or ‘rule-of-thumb’ that can be relied on to select the flow category for use in defining a flow recommendation (see Table 10). Comparative studies between Tennant and more site-specific studies would suggest that flow criteria between the 30 percent and 60 percent ranges of MAF are common (Wesche 1973, Wood and Whelan 1962, Joy et al., 1981, Orth and Maughan 1981, Prewitt and Carlson 1979, Nelson 1980). It recognized that many of these applications targeted species and river systems that are very different from the Scott River, but remain roughly consistent across species and systems. Nelson (1980) suggests that the Tennant Method may in some instances overestimate instream flow requirements compared to site-specific analyses in larger river basins. However, this is not known to be generally true across a variety of systems. Fundamentally, the use of Tennant for estimating minimum instream flows remains widely applied and accepted. Given the objectives of this analysis and a desire to maintain a conservative view toward protection of the aquatic resources within the Scott River, an 80 percent basis of MAF was selected for use in this application of Tennant. This represents the mid-point of the Optimal Range for protection (Table 8). This percent of the mean annual flow was partitioned between all months within the year based on the percent distribution of Historical mean monthly flows (Table 9). In this
28
instance, the application of the Tennant Method was ‘modified’ to allow the hydrograph to mimic natural flows patterns as is commonly undertaken with this technique for adjustment of seasonal flow patterns (e.g., Ott and Tarbox 1977, Bayha 1978, Estes 1985, Fernet 1987, Trihey 1996). The resulting instream flow values are provided in Table 9. Table 9. Estimated monthly instream flows based on application of the Tennant using the
mid-point of the Optimum Range or 0.8 of the MAF.
Washington Base Flow Method: This methodology estimates the required instream flow levels based on a ranking of the stream in terms of wildlife, fisheries, scenic and esthetic, water quality, navigational, and other environmental values. The technique is applicable to salmonid systems. The average rating is then used in a nomographic solution to obtain a flow-duration percentile. This flow-duration percentile is then used to estimate the flow recommendation using the flow duration curve for the river. In the absence of site specific rankings in each of these categories, the highest stream ranking (i.e., 24) was chosen and the solution for Western Washington during the low flow period was selected for use with this technique. This choice is justified given the high value fisheries and the importance of this river for overall environmental concerns to tribal trust resources. The resulting flow-duration statistic would be the 60 percent exceedance. This basic technique was modified for this report to utilize the 60 percent exceedance value on a monthly basis in order to preserve the natural pattern of seasonal flows. The monthly 60 percent flow exceedance values based on the daily discharges at Fort Jones for the 1942-1971 period of record were used for this analysis. The preservation of the seasonal pattern of natural flows is considered important in light of the flow dependent cues of anadromous species to flow timing in the main stem in conjunction with tributary flows. The resulting instream flow estimates from this technique are provided in Table 10.
29
Table 10. Estimated monthly instream flows based on application of the Washington Base Flow Method.
Hydraulic Analysis: The study site selection for collection of adult fall chinook site specific passage data was based on previous observations of adults holding in the pool directly below the site, during low water conditions (Figure 17). Northing, easting, elevation, and roughness data were recorded along the top of the shallow riffle. The riffle is located at 41 42’ 25.13”N, 123 01’ 28.87”W. Vertical selections across the transect line occurred when the surveyors observed significant changes in depths, substrates and velocities. Water surface elevations were collect at each water’s edge, and other random locations across the transect line. A survey grade total station, using standard survey techniques, was used to collect the northing, easting, and elevation data. The Scott River discharge was collected at the study site, during the period of cross section survey, in order to relate the water surface elevation for the cross section to the stream discharge. The cross section location was chosen based on limited inter-gravel flow, laminar flow, small substrate, and a relatively u-shaped channel (Figure 18). Twenty verticals were measured for water depth, distance from the left bank, with cell velocities being collected using a calibrated Price AA meter. A temporary stream gage was placed at the study sit and monitored throughout the data collection effort ensure the stream discharge remained static during the entire data collection period.
30
Figure 17. Survey transects were located on the Scott River at rkm 11.0, approximately
0.75 rkm upstream of McGuffy Creek.
Figure 18. Study site transect locations for collection of discharge and cross section geometry data.
WinXSPro was calibrated to the field based cross section geometry, water surface elevation and discharge (Figure 19, Table 11). The resulting stage discharge relationship was used in PHABSIM.
31
970.0
970.5
971.0
971.5
972.0
972.5
973.0
973.5
974.0
Ele
vatio
n (fe
et)
x-distance (feet)
Elevation (feet) Water Surface Elevation Figure 19. Scott River geometry and water surface elevation at 105 cfs. Table 11. Example calibration results for WinxsPro.
Substrate was ignored and binary depth and velocity passage criteria were adopted from Thompson (1972):
• Depth < 0.79 ft; Suitability = 0.0 • Depth > 0.79 ft; Suitability = 1.0 • Velocity < 8.0 ft/s; Suitability = 1.0 • Velocity > 8.0 ft/s; Suitability = 0.0
What the analysis indicates is that flows above ~40 cfs are required to allow at least 50% of the channel width to be passable and that at about ~90 cfs represents an asymptotic range of 80-90% of the channel width in which passage is available. The resulting simulated changes in stage and velocity profiles were integrated with the binary passage criteria above to estimate the amount of passage habitat as a function of discharge and normalized to the stream wetted surface area (Figure 20).
32
20
30
40
50
60
70
80
90
20 40 60 80 100 120 140 160 180 200
Habitat versus Flow
Hab
itat a
s Per
cent
of S
trea
m S
urfa
ce A
rea
Discharge Figure 20. Normalized percent of passage area as a function of discharge (cfs).
Combined Passage Estimates The various estimated monthly instream flows from all the hydrologic methods above were averaged to obtain a single monthly instream flow recommendation (MIFR, Table 12). Table 12. Averaged instream flow methods and the Minimum Instream Flow
Recommendation (MIFR) in cfs and MIFR and the USFS for the Scott River Canyon.
Oct 76 40Nov 147 200Dec 462 200Jan 581 200Feb 756 200Mar 630 200Apr 730 150May 700 150Jun 366 125Jul 102 50Aug 58 30Sep 57 30
Month MIFR (cfs) USFS (cfs)
33
California Department of Fish and Wildlife Recommended Interim Instream Flows In response to comments, the California Department of Fish and Wildlife (CDFW) provided their supported interim passage and physical habitat instream flow recommendation for the Scott River at the USGS streamflow gauge 11519500 near Fort Jones, CA. Their recommended instream flows are intended to provide interim protection for the Scott River’s migrating, spawning, and rearing life stages of salmon and steelhead. The CDFW utilized separate hydrology based methodologies in support of their instream flow recommendations.
Passage The California Department of Fish and Wildlife used the Qfp regression formula contained in R2 Resources (2008) for the determination of minimum fish passage flows, in support to the California State Water Resources Control Board, where:
Qfp = 19.3QmDmin2.1DA-072
Whereas: Qfp is the minimum the minimum fish passage flow (cfs), Qm is the mean annual flow, Dmin is the minimum passage depth criterion, and DA is the drainage area.
Spawning and Juvenile Rearing Interim minimum instream flows necessary to support the Scott River salmon and steelhead spawning and juvenile rearing life stages were estimated using the Hatfield and Bruce (2000) regression equations for the latitude and longitude of the USGS Scott River gage 11519500 located near Fort Jones, CA. The regression equations used mean annual discharge, latitude, and/or longitude to determine the appropriate flows for salmon and steelhead life stages, including spawning and juvenile rearing. The CDFW utilized Tessmann’s adaptation of the Tennant Method to further account for the hydrology of the Scott River watershed. Whereas, for any given month, if the mean monthly flow is less than 40% of the mean annual flow, the prescribed flow is set at the mean monthly flow. If the mean monthly flow is greater than the mean annual flow, the prescribed flow is set at 40% of the mean monthly flow. Otherwise, the prescribed flow is set at 40% of the mean annual flow.
CDFG Recommended Interim Minimum Instream Flow The final recommended interim minimum instream flow was derived by taking the lesser of the minimum flows developed using the Qfp and Hatfield & Bruce (2000), and the Tessmann’s adaptation of the Tennant Method. During periods when Scott River flow drops below the interim thresholds, the natural flow becomes the prescribed minimum (Table 13).
34
Table 13. The CDFW recommended minimum, interim instream flows for the Scott River at the USGS streamflow gauge 11519500 near Fort Jones, CA.
Oct 1 - 15 Apr 1 - 15Oct 16 - 31 Apr 16 - 30Nov 1 - 15 May 1 - 15Nov 16 - 30 May 16 - 31Dec 1 - 15 Jun 1 - 15Dec 16 - 31 Jun 16 - 30Jan 1 - 15 Jul 1 - 15Jan 16 - 31 Jul 16 - 31Feb 1 - 14 Aug 1 - 15Feb 15 - 28 Aug 16 - 31Mar 1 - 15 Sep 1 - 15Mar 16 - 31 Sep 16 - 30
*Natural Flow
6262
1651651651347777
Date CDFW (cfs or *NF)134134165165
362362362362354354
134140266266337337
Date CDFW (cfs or *NF)
The CDFW flows are fairly similar to the MIFRs during the adult Chinook migration period (September through December). Figure 19 provides a visual comparison between CDFW, MIFR, and USFS recommended minimum instream flow requirements. The CDFG flows were slightly higher during the September through November period, with the MIFRs being slightly higher during December. All the recommended interim flows show an increasing trend consistent with the natural hydrograph and historical mean monthly flow.
0
20
40
60
80
100
120
140
160
Sep 1 – 15 Sep 16 – 30 Oct 1 – 15 Oct 16 – 31
Dis
char
ge (c
fs)
Bi-weekly period
MIFR CDFW USFS MAF
050
100150200250300350400450500
Nov 1 – 15 Nov 16 – 30 Dec 1 – 15 Dec 16 – 31
Dis
char
ge (c
fs)
Bi-weekly period
MIFR CDFW USFS MAF
Figure 21 Comparison between CDFW, MIFR, USFS Instream flow
recommendations, and mean monthly flow for the period 1942-1971, for the periods September-October and November-December.
35
Summary and Conclusions This report uses a variety of methods to achieve a comprehensive minimum instream flow recommendation (MIFR) for the Scott River below the USGS gauging station near Fort Jones, CA for the purposes of protecting and enhancing salmonid stocks in the Scott River. The results of this report largely agree with the results of a previously completed CDFW analysis, and the two primary methods used in this report (site-specific hydraulic analysis and a range of hydrologic methods) largely agree with each other. The resulting minimum MIFR for the Scott River below the USGS gauging station near Fort Jones presented in Table 11 are interim recommendations based on a variety of valid hydrology based modeling approaches used for estimating minimum flow regime requirements using hydrology and limited site specific data. The hydrology based methods agree with the hydraulic based passage criteria where flows above about ~80 cfs provide increasing areas of the wetted width available for passage of adult salmonids to spawning grounds. The following table is a summary of the life-stage periodicities for the critical salmonid life-stages (Table 12). Obviously, precipitation and runoff will dictate the Scott River flows during months with insignificant diversions and groundwater recharge. However, the MIFR should be met during and immediately after times of year with water diversions and pumping. The recommended monthly interim flows are considered necessary, in order to provide minimal, subsistence level fishery conditions. These conditions include adult migration, spawning, egg incubation, rearing, downstream migration, and the summer survival of the anadromous fish, for the Scott River Canyon reach, located below the USGS gage, near Fort Jones. These minimal conditions and resulting MIFR should only be experienced during critically dry years, without resulting in the further depletion of the Scott River fishery resources. During wetter water years, flows should be maintained above the MIFR, accordingly, in order to provide the basic habitat and life history needs of the aquatic resources necessary for the recovery of the Scott River fisheries, given the present environmental conditions of the watershed. The MIFR presented in Table 11 are the basis or starting point for the ongoing, site specific instream flow studies to build upon. In the interim, the MIFRs are intended to protect salmonid populations of the Scott River. The Scott River juvenile Chinook production for the 2006 outmigration season was the lowest observed since CDFW began sampling in 2000 (Figure 19). The CDFW authors (Chesney et al., 2007) believe that the lower numbers were attributed to high mortalities of incubating eggs during the December 31, 2005 high flow event, when the recorded discharge at the USGS gage near Fort Jones reached over 20,000 cfs. However, the recorded discharge at Fort Jones was only 13 cfs that September, during a period when the adult Chinook begin their upstream migration (Figure 20, Table 3). The late December 2005 event was most likely of sufficient magnitude to cause significant
36
bedload movement that scoured out the Chinook redds and incubating eggs throughout the Scott River Canyon and Valley reaches (Chesney et al., 2007).
Figure 22. Scott River juvenile Chinook production estimates for years 2000-2006 (Chesney et al., 2007).
20,300
1
10
100
1,000
10,000
100,000
9/1/
05
9/15
/05
9/29
/05
10/1
3/05
10/2
7/05
11/1
0/05
11/2
4/05
12/8
/05
12/2
2/05
Date
Disc
harg
e (c
fs)
Figure 23. U.S. Geological Survey time-series daily discharge for the Scott River near Fort Jones, CA. Site: 11519500 September 1 – December 31, 2005, logarithmic scale.
The collection of hourly discharge, weir counts, and temperature data (Figure 21 and Figure 22), along with site specific biological, topographic, and hydraulic evaluations will be invaluable towards refining the flow requirements for the varying species and life
37
stages within the Canyon reach of the Scott River. Additional site specific evaluations and modeling will also be necessary for Scott River mainstem reaches above the Canyon reach, as well as the tributaries to the Scott River where diversions occur.
0
5
10
15
20
25
9/1/2008
9/8/2008
9/15/200
8
9/22/200
8
9/29/200
8
10/6/2
008
10/13/20
08
10/20/20
08
10/27/20
08
Date
Aver
age
daily
wat
er te
mpe
ratu
re
(oC)
0
50
100
150
200
250
Num
ber o
f adu
lt Ch
inoo
k sa
lmon
Chinook passing weir Temperature
Figure 24. Average daily water temperature measured at the mouth of the Scott River
and daily counts of adult Fall Chinook enumerated at the CDFW weir (rkm 29.3) during the fall of 2008.
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Chinook passing weir Discharge (cfs)
Figure 25. Scott River discharge measured at USGS Scott River near Fort Jones, CA.
and daily counts of adult Fall Chinook enumerated at the CDFW weir (rkm 29.3) during the fall of 2008.
Historically, within the Canyon reach, flows were sufficient during the adult salmonid migration period to allow unimpeded access to upper reaches of the Scott Valley and tributaries. Spawning within the confined Canyon reach was avoided; since the adults most likely imprinted to the upper Valley and tributaries. Spawning in the Canyon reach was likely detrimental in years that had subsequent high flow events, due to high water
38
velocities and bedload scour potential at redd sites. These events cause high mortalities of incubating eggs and emergent fry. Within the historical Scott Valley prior to large-scale channelization, flood flows could overtop the river’s banks into the natural floodplain. The stream’s power decreased as it expanded over the large, flat areas across the valley. The highly sinuous, multiple braided channel and active floodplain greatly diminished the channel velocities and bedload scour within the spawning areas. The floodplain also provided an expansive, shallow, and low velocity refuge for the newly emergent fry. However, most of the present day’s Scott Valley reach was artificially straightened and confined into a single channel, with armored banks, in an effort to contain the river and decrease meandering during high flow events. This confinement and decreased sinuosity greatly increased the stream power along the thalweg and margins resulting in abnormally high bedload scour potential and mortality of both the incubating eggs and newly emergent fry. The final MIFRs are not intended to ensure habitat conditions for the mainstem reaches above the Scott River Canyon reach, located downstream of the USGS gage near Fort Jones, and tributaries to the mainstem Scott River are meeting their specific minimum instream flow requirements. However, in order to meet the MIFRs for the Scott River Canyon reach, especially during critically dry years, we assume that the habitat conditions for the mainstem and tributaries above the Canyon will be favorable, when comparing to the existing conditions. In comparison, the CDFW and MIFRs recommended minimum interim Scott River instream flows that are fairly similar during the adult salmon migration period. The CDFW recommendations are higher during the September through November period, with the MIFRs being a little higher during December. References Bayha, K.D. 1978. Instream flow methodologies for regional and national assessments.
Instream Flow Information Paper No. 7. FWS/OBS 78/61. Ft. Collins, CO. California Dept. of Fish and Game. 2009. Chinook salmon reconnaissance survey on the
Scott River. Memorandum. September 28, 2009. 3 pp. California Department of Fish and Wildlife (CDFG). 2010. Development of Interim
Flow Recommendations for Protection of Fishery Resources in the Scott River Watershed, Siskiyou County. Northern Region Fisheries Branch. 38 pp.
California Department of Water Resources. 1991. Scott River Flow Augmentation Study.
State of Calif. The Resource Agency, Dept. of Water Resources, Northern District. 137 pp.
39
Chesney W.R., B.J. Cook, W.B. Crombie, H.D. Langendorf and J.M. Reader. 2007.
Shasta and Scott River Juvenile Outmigration Study. Annual Report. State of California, the Resources Agency, Department of Fish and Game. Anadromous Fisheries Resource Assessment and Monitoring Program 68 pp.
Clayton T.L. 2006. 2005 Fall Chinook Salmon Spawning Ground Survey. USDA Forest
Service Klamath National Forest. Fort Jones, CA. 39 pp. Estes, C.C. 1985. Evaluation of methods for recommending instream flows to support
spawning by salmon. Thesis submitted for Master of Science, Washington State University.
Fernet, D.A. 1987. A comparison of the Weighted Usable Width, Modified Tennant and
Instream flow Incremental Methodology Analysis of Instream Flow Needs in Pekisko Creek. Environmental Management Associates, Calgary, Alberta.
Goode J.R., J.M. Buffington, D. Tonina, D.J. Isaak, R.F. Thurow, S.D. Wenger, D.
Nagel, C. Luce, D. Tetzlaff, and C. Soulsby. 2013. Potential effects of climate change on streambed scour and risks to salmonid survival in snow-dominated mountain basins. Hydrological Processes. 27, 750–765
Hardy, T.B. and R.C. Addley. 2006. Evaluation of Interim Instream Flow Needs in the
Klamath River, Phase II, Final Report. Report prepared for USDI. Institute for Natural Systems Engineering. Utah Water Research Laboratory. Utah State University. Logan UT. July 31, 2006. 304pp.
Hasler, C.T., B. Mossop, D.A. Patterson, S.G. Hinch, and S.J. Cooke 2012. Swimming
activity of migrating Chinook salmon in a regulated river. Aquatic Biology. Vol. 17: 47–56.
Hatfield, T. and J. Bruce. 2000. Predicting salmonid habitat-flow relationship for streams
from western North America. North American Journal of Fisheries Management 20 (4):1005-1015.
Hinch S.G., S.J. Cooke, M.C. Healey, and A.P. Farrell. 2006. Behavioral physiology of
fish migrations: salmon as a model approach. In: Sloman K, Balshine S, Wilson R (eds) Fish physiology, Vol 24: behavioral and physiology of fish. Academic Press, London, p 239−295.
Joy, E.T. Jr., et al., 1981. An evaluation of instream flow methods for use in West
Virginia. Report from Division of Wildlife Resources, West Virginia Department of Natural Resources, to Ohio River Basin Commission, Cincinnati, Ohio.
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Knechtle M. and D. Chesney. 2011. 2010 Scott River Salmon Studies Final Report. California Department of Fish and Game, Northern Region, Klamath River Project. Yreka, California 21 pp.
Mack, S. 1958. Geology and Ground-Water Features of Scott Valley, Siskiyou County,
California. U.S. Geological Survey Water-Supply Paper 1462. Washington, DC: U.S. Government Printing Office. 98 pp.
Maurer S. 2002. Scott River Watershed Adult Coho Salmon Spawning Survey December
2001- January 2002. Contract to the USDA, Forest Service, Klamath National Forest, Scott River Ranger District, Fort Jones, California. 32 pp.
Mesa M.G. and C.D. Magie. 2004. Evaluation of energy expenditure in adult spring
Chinook salmon migrating upstream in the Columbia River basin: an assessment based on sequential proximate analysis. U.S. Geological Survey Biological Resources Discipline, Western Fisheries Research Center, Columbia River Research Laboratory.
Neitzel, D.A., Becker, C.D., 1985. Tolerance of eggs, embryos, and alevins of Chinook
salmon to temperature changes and reduced humidity in dewatered redds. Transactions of the American Fisheries Society 114, 267e273.
Nelson, F.A. 1980. Evaluation of selected instream flow methods in Montana. In:
Proc.60th Ann. Conf. Western Assoc. Fish and Wildlife Agencies, pp. 412-432. NRC. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of
Decline and Strategies for Recovery Committee on Endangered and Threatened Fishes in the Klamath River Basin, National Research Council. ISBN: 0-309-52808-9, 424 pp.
North Coast Regional Water Quality Control Board (Regional Water Board) 2005. Staff
Report for the Action Plan for the Scott River Watershed Sediment and Temperature Total Maximum Daily Loads.
Orth, D.J. and O.E. Maughan. 1981. Evaluation of the “Montana Method” for
recommending instream flows in Oklahoma streams. Proc. Okla. Acad. Sci. 61:62-66.
Ott, A.G. and K.E. Tarbox. 1977. “Instream flow” applicability of existing methodologies
for Alaskan waters. Final Report prepared for Alaska Department of Fish and Game.
Patterson, D. 1976. Evaluation of habitats resulting from stream bank protection projects
in Siskiyou and Mendocino Counties, California. U.S. Soil Conservation Service, Red Bluff, 15p.
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Prewitt, C.G. and C.A. Carlson. 1979. Evaluation of four instream flow methodologies used on the Yampa and White Rivers, Colorado. U.S. Dept. of Interior, Bureau of Land Management, Biological Sciences Series No. 2, Denver, CO.
Quigley D, S. Farber, K Conner, J. Power, and L. Bundy. 2001. Water Temperatures in
the Scott River Watershed in Northern California. Siskiyou Resource Conservation District, Timber Products Company, Fruit Growers Supply Company, U.S. Forest Service- Klamath National Forest, and Natural Resources Conservation Service. 67 pp.
Quiñones R. 2005. Mid-Klamath River Chinook Spawner Escapement Surveys. U.S.
Forest Service, Klamath National Forest. FWS Agreement # 81335H014. 40 pp. R2 Resource Consultants, Inc. and Stetson Engineers, Inc., 2008. North Coast Instream
flow Policy: Scientific Basis and Development of Alternatives Protecting Anadromous Salmonids.
Shaw, T.A., C. Jackson, D. Nehler, and M. Marshall. 1998. Klamath River (Iron Gate
Dam to Seiad Creek) Life Stage Periodicities for Chinook, Coho, and Steelhead. USDI-Fish and Wildlife Service, Coastal Calif. Fish and Wildlife office, Arcata, CA. 43 pp. + appendices.
Snyder, J.O. 1931. Fish Bulletin No. 34. Salmon of the Klamath River California. I. The
Salmon and the Fishery of Klamath River. II. A Report on the 1930 Catch of King Salmon in Klamath River. Fish Bulletin, Scripps Institution of Oceanography Library, Scripps Institution of Oceanography, UC San Diego. 130 pp.
S, S. Papadopulos and Associates, Inc. 2012. Groundwater Conditons in Scott Valley,
California. Prepared for the Karuk Tribe. 130 pp. Strange, J.S. (2012): Migration Strategies of Adult Chinook Salmon Runs in Response to
Diverse Environmental Conditions in the Klamath River Basin, Transactions of the American Fisheries Society, 141:6, 1622-1636
Thompson, K. E. 1972: Determining streamflows for fish life. Proceedings of the
instream flow requirements workshop, Pacific Northwest River Basins Commission, Portland, Oregon : 31-50.
Trihey and Associates, INC. 1996. Instream flow requirements for tribal trust species in
the Klamath River. 43pp. USFWS. 1999. Trinity River flow evaluation. Final Report. 308pp + Appendices Van Kirk, Robert W. and Seth W. Naman, 2008. Relative Effects of Climate and Water
Use on Base-Flow Trends in the Lower Klamath Basin. Journal of the American
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Water Resources Association (JAWRA) 44(4):1035-1052. DOI: 10.1111/j.1752-1688.2008.00212.x
West, J.R., O.J. Dix, A. Olson, M.V. Anderson, and J.H. Power, 1990. Evaluation of fish
habitat condition and utilization in Salmon, Scott, Shasta, and Mid-Klamath sub-basin tributaries 1988/89. USDA Forest Service, Yreka, Calif. 96097. Under contract with USFWS Klamath Field Office, Yreka, Calif. no. 14-16-0001-89508.
Wesche, T.A. 1973. Parametric determination of minimum streamflow for trout. Water Resources Series No. 37, Water Resour. Res. Inst., Univ. of Wyoming, Laramie, WY. West J.R. 1991. A Proposed Strategy to Recover Endemic Spring-run Chinook Salmon
Populations and Their Habitats in the Klamath River Basin. File Reprot, U.S. Department of Agriculture Forest Service, Pacific South West Region. 25 pp.
Wood, R.K., and D.E. Whelan. 1962. Low-flow regulation as a means of improving
stream fishing. In: Proc. 16th Ann. Conf. SE Assoc. of Game and Fish Commissioners, Charleston, SC.
Yokel, E. 2008. Monitoring Report-2008. Scott River Water Trust. Siskiyou Resource
Conservation District. Etna, CA. 48 pp.
