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Emily J. Cooper1, Alison P. O’Dowd, and James J. Graham, Humboldt State University, 1 Harpst Street, Arcata, California 95521 Darren W. Mierau, California Trout, 615 11th Street, Arcata, California 95521 William J. Trush, Humboldt State University, 1 Harpst Street, Arcata, California 95521 and Ross Taylor, Ross Taylor and Associates, 1660 Central Avenue # B, McKinleyville, California 95519 Salmonid Habitat and Population Capacity Estimates for Steelhead Trout and Chinook Salmon Upstream of Scott Dam in the Eel River, California Abstract Estimating salmonid habitat capacity upstream of a barrier can inform priorities for fisheries conservation. Scott Dam in California’s Eel River is an impassable barrier for anadromous salmonids. With Federal dam relicensing underway, we demonstrated recolonization potential for upper Eel River salmonid populations by estimating the potential distribution (stream-km) and habitat capacity (numbers of parr and adults) for winter steelhead trout (Oncorhynchus mykiss) and fall Chinook salmon (O. tshawytscha) upstream of Scott Dam. Removal of Scott Dam would support salmonid recovery by increasing salmonid habitat stream-kms from 2 to 465 stream-km for steelhead trout and 920 to 1,071 stream-km for Chinook salmon in the upper mainstem Eel River population boundaries, whose downstream extents begin near Scott Dam and the confluence of South Fork Eel River, respectively. Upstream of Scott Dam, estimated steelhead trout habitat included up to 463 stream-kms for spawning and 291 stream-kms for summer rearing; estimated Chinook salmon habitat included up to 151 stream-kms for both spawning and rearing. The number of returning adult estimates based on historical count data (1938 to 1975) from the South Fork Eel River produced wide ranges for steelhead trout (3,241 to 26,391) and Chinook salmon (1,057 to 10,117). An approach that first estimated juvenile habitat capacity and then used subsequent life stage survival rates yielded 1,281 (CV 56%) steelhead trout and 4,593 (CV 34%) Chinook salmon returning adults. Variability in estimated fish numbers reflects application of densities and survival rates from other populations, assumptions about salmonid productivity in response to potential spawning habitat capacity, residency and outmigration of early life-stages, summertime water quality conditions, and inter-annual hydrograph, marine, and population variability. Keywords: Eel River, salmonid, habitat, dam Introduction in successful recolonization on several accounts (Pess et al. 2003, 2012; Brewitt 2016). Homing Large flood control and hydroelectric dams have instincts are documented for most anadromous contributed to freshwater habitat degradation salmonids (Quinn 1993), but straying from the and fish population declines through watershed return to natal streams is also well documented fragmentation, disruption of natural flow regimes, (Hendry et al. 2004; Quinn 2005; Keefer et al. interference with nutrient distribution, and block- 2005, 2008). Straying from a natal stream is con- age from historical spawning and rearing habitat sidered an ecological and evolutionary mechanism (Sheer and Steel 2006). Efforts to remove dams as for population persistence (Cooper and Mangel barriers to fish passage and reconnect migratory fish 1999, Hill et al. 2002, Hilborn et al. 2003) and is to suitable stream habitat has eventually resulted hypothesized to initially increase in response to an increase in disturbance regime and habitat avail- ability, such as from dam removal (Quinn 1984). 1Author to whom correspondence should be addressed. Located in northern California, the upper main- Email: [email protected] stem Eel River is considered the area upstream 70 Northwest Science, Vol. 94, No. 1, 2020 © 2020 by the Northwest Scientific Association. All rights reserved. of its confluence with the Middle Fork Eel River, restored migratory access (Hanrahan et al. 2004, where the National Marine Fisheries Service Winter and Crain 2008, Roni et al. 2010). (NMFS) identified the Northern California (NC) Past efforts to quantify the amount of blocked Steelhead trout (Oncorhynchus mykiss) and Cali- salmonid habitat in the mainstem Eel River up- fornia Coastal (CC) Chinook salmon (O. tshawyts- stream of Scott Dam and its potential population cha) populations as Ecologically Significant Units production involved various methods with coarse (ESU) (NMFS 2016). Near the headwaters of habitat measurements, resulting in estimates rang- the upper mainstem Eel River is a water storage, ing from 50 to 400 km of habitat (CDFG 1979, diversion, and hydropower facility known as the VTN 1982, USFS and BLM 1995, Becker and Potter Valley Project (PVP). The PVP includes Reining 2009, NMFS 2016). However, all of these two dams—Cape Horn Dam, a run-of-the-river studies acknowledge that fall Chinook salmon and dam with a fish ladder, and 19 river-km upstream winter steelhead trout would potentially benefit from Cape Horn Dam is Scott Dam, a water stor- from restored access to habitat above Scott Dam. age dam with no fish passage. Impacts from the Other anadromous salmonids native to the Eel PVP in combination with other anthropogenic River are less likely to use habitats above Scott impacts in the basin have resulted in degradation Dam, as evidenced by sparse observations over of the Eel River’s aquatic habitat (O’Farrell et the past few decades of Coho salmon (O. kisutch), al. 2012), and native salmonid populations have and no observations of coastal cutthroat trout (O. declined to an estimated 1 to 3% of their historic clarkii) at Cape Horn Dam’s fish passage facil- levels (Yoshiyama and Moyle 2010). Upper Eel ity, Van Arsdale Fisheries Station (VAFS) (PVID River ESUs including NC steelhead trout and CC 2017). This portion of the watershed extends be- Chinook salmon have the potential to become a yond present Coho salmon and coastal cutthroat recolonization resource to newly opened habitat trout distribution (Xanthippe 2004). upstream of Scott Dam upon barrier removal. In this study, we quantified extent of suitable Since its construction in 1922, Scott Dam of habitat and its capacity for steelhead trout and the PVP has blocked fish passage to upstream Chinook salmon above Scott Dam. Field habitat habitat historically used by anadromous salmonids, sampling, habitat suitability models, and historical including fall-run Chinook salmon and winter-run fish count data were used in estimating potential steelhead trout (NMFS 2016). Genetic integrity stream capacities for different life stages of steel- and resiliency of migratory populations such as head trout and Chinook salmon. The challenge anadromous salmonids rely on access to uninter- of predicting salmonid production in habitat rupted spawning and rearing streams (Moyle et al. 2017). As salmonid populations throughout not currently available to those species required Pacific Coast watersheds have been listed under modeling from salmonid populations in other the Federal Endangered Species Act, fisheries man- areas. Quantifying salmonid habitat suitability agement has responded with recovery strategies and its capacity for an expected long term average involving passage and habitat restoration to allow population must reflect biological requirements anadromous salmonids to recolonize their ancestral at different life stages and stream environment habitats (Pess et al. 2008, NMFS 2016). Beyond conditions as they vary spatially and temporally. the presence and condition of nearby salmonid Linking the biology and habitat requirements of populations, recolonization potential upstream of salmonids to habitat conditions and identifying Scott Dam for those ESUs also depends on habitat limiting factors for potential salmonid production suitability and capacity in tune with each colonist should therefore be incorporated into modeling species’ life history variants (Pess et al. 2014). potential stream habitat capacity in prioritized Consequently, salmonid passage restoration and watersheds (Anlauf-Dunn et al. 2014). recolonization often involves efforts to predict the Hydraulic units of suitable stream habitat suitability of potentially reopened habitat and the change seasonally and with different biological increase in salmonid production resulting from phases of a species. Adult salmonid habitat is often Salmonid Habitat Above Scott Dam 71 measured in units of stream length with suitable ing fish passage above Scott Dam (NMFS 2016). spawning habitat and related to number of fish Initiation of the PVP Federal Energy Regulatory observed or expected to occur in those stream Commission (FERC) relicensing process in 2017 lengths to calculate fish capacity. Alternatively, underscored the opportunity and need to quantify because salmonids occupy different habitat type salmonid habitat extent and potential production units (e.g., pools, riffles, flatwater, etc.) at certain capacity upstream of Scott Dam, and provided a times of year, habitat capacity can also be quanti- primary impetus for this study. The information fied by the availability of habitat types and the presented here will aid fisheries managers in as- number of fish observed or expected to occur in sessing whether restoring salmonid access to the those habitat types. For example, the distribu- area is merited. tion and proportion of habitat type units within a stream reach at summer base flows can be used Methods to approximate the quantity of rearing habitat Study Area for summertime-rearing juvenile steelhead trout (Agrawal et al. 2005).

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