Habitat studies

Yoshiyama, R. M., & Moyle, P. B. (2010). Historical review of Eel River anadromous salmonids, with emphasis on Chinook salmon, coho salmon and steelhead. University of California, Center for Watershed Sciences.

Yoshiyama Moyle Historical Review of Eel River Anadromous Salmonids Final Report 2010 (pdf)

Abstract:  “The Eel River basin once possessed significant populations of at least five distinct kinds of anadromous salmonids, including fall-run Chinook salmon, coho salmon, winter and summer steelhead, and coastal cutthroat trout. In addition, there were small populations of chum and pink salmon and possibly spring Chinook salmon. It is likely that an even greater number of seasonal runs or life-history variants within some species previously co-existed in the Eel River system. The historical plenitude of salmon in the Eel River motivated the establishment of a commercial salmon fishery as early as 1854, along with associated canning operations. Salmon canneries operated on the Eel River during the late-19th and early-20th centuries, producing a peak output of 15,000 cases of canned salmon during 1883. The cannery data can be roughly translated into minimal population estimates which average about 93,000 fish per year during the period 1857-1921 and evidently approached 600,000 fish in the peak year 1877, mostly Chinook salmon. Given that the cannery records result in a very conservative estimate of Chinook numbers, the records suggest that historic runs of Chinook salmon probably ranged between 100,000 and 800,000 fish per year, declining to roughly 50,000-100,000 fish per year in the first half of the 20th century.”

Emily J. Cooper, Alison P. O’Dowd, James J. Graham, Darren W. Mierau, William J. Trush, Ross Taylor (2020)  “Salmonid Habitat and Population Capacity Estimates for Steelhead Trout and Chinook Salmon Upstream of Scott Dam in the Eel River, California.” Northwest Science. 94(1), 70-96

Cooper et al 2020 (pdf)

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.”

FitzGerald, Alyssa M., David A. Boughton, Joshua Fuller, Sara N. John, Benjamin T. Martin, Lee R. Harrison, and Nathan J. Mantua. (2022) “Physical and biological constraints on the capacity for life-history expression of anadromous salmonids: an Eel River, California, case study.” Canadian Journal of Fisheries and Aquatic Sciences. 99(999), 1-19

Fitzgerald et al 2022 (pdf)

Abstract: “Recovery of anadromous salmonid populations is complicated by their complex life histories. We examined the spatiotemporal interplay of stream temperature, geomorphic features, and a species’ thermal sensitivity mediated by bio- logical interactions in a case study of steelhead trout (Oncorhynchus mykiss) and Chinook salmon (Oncorhynchus tshawytscha) in California’s Eel River watershed. We estimated habitat suitability and fish capacity for each salmonid run and freshwater life stage during average, cool, and warm years in each of the watershed’s subbasins, including a historically occupied high- elevation subbasin upstream of an impassable dam. Our estimates varied depending on whether we accounted for exposure to the Sacramento pikeminnow (Ptychocheilus grandis), an introduced predator and competitor. Our results indicate that the dammed subbasin has substantial salmonid capacity relative to the rest of the watershed and could provide an important cool-water refuge during warm years and from pikeminnow, potentially improving the productivity and resilience of multiple anadromous salmonid populations. Our approach can be applied in any setting where spatially explicit habitat metrics can be estimated and population-specific and life-stage-specific habitat criteria can be specified.”

Other Background documents

Samantha H Kannry, Sean M O’Rourke, Suzanne J Kelson, Michael R Miller, (2020) “On the Ecology and Distribution of Steelhead (Oncorhynchus mykiss) in California’s Eel River.” Journal of Heredity. 111(6), 548–563

Kannry et al 2020 (pdf)

The preservation of life history and other phenotypic complexity is central to the resilience of Pacific salmon stocks. Steelhead (Oncorhynchus mykiss) express a diversity of life-history strategies such as the propensity to migrate (anadromy/residency) and the timing and state of maturation upon return to freshwater (run-timing), providing an opportunity to study adaptive phenotypic complexity. Historically, the Eel River supported upwards of 1 million salmon and steelhead, but the past century has seen dramatic declines of all salmonids in the watershed. Here we investigate life-history variation in Eel River steelhead by using Rapture sequencing, on thousands of individuals, to genotype the region diagnostic for run-timing (GREB1L) and the region strongly associated with residency/anadromy (OMY5) in the Eel River and other locations, as well as determine patterns of overall genetic differentiation. Our results provide insight into many conservation-related issues. For example, we found that distinct segregation between winter and summer-run steelhead correlated with flow-dependent barriers in major forks of the Eel, that summer-run steelhead inhabited the upper Eel prior to construction of an impassable dam, and that both life history and overall genetic diversity have been maintained in the resident trout population above; and we found no evidence of the summer-run allele in the South Fork Eel, indicating that summer run-timing cannot be expected to arise from standing genetic variation in this and other populations that lack the summer-run phenotype. The results presented in this study provide valuable information for designing future restoration and management strategies for O. mykiss in Northern California and beyond.

Upper Eel River temperature monitoring

Native Fish Society

Eel River action plan

Eel River Action Plan 2016 (pdf)

The Eel River ecosystem, its salmon and steelhead populations, and other native fish and wildlife populations have been in decline for the past century and a half. It has been transformed from one of the most productive river ecosystems along the Pacific Coast to a degraded river with heavily impaired salmonid populations. The mission of the Eel River Forum is to “coordinate and integrate conservation and recovery efforts in the Eel River watershed to conserve its ecological resilience, restore its native fish populations, and protect other watershed beneficial uses.” The Forum was convened in July 2012 and adopted its charter in June 2013.

The purpose of this document is to provide a summary description of issues the Eel River Forum has agreed are primary factors impairing salmonid recovery and ecological health of the Eel River. See p. 56 for the Potter Valley Project section.

2018 Capital Modifications Report

In 2018, Sonoma Water commissioned a high-level feasibility study of potential alternatives for capital modifications to the Potter Valley Project. While additional studies have since built on this initial report, the study considers alternatives, discusses the advantages and disadvantages for each and provides rough costs for each. Additional, finer scale alternatives analysis can be found in the Phase 2 Studies.

  1. Cap Mod cover letter (pdf)
  2. Capital modifications feasibility report  (pdf)
  3. Evaluation of sediment stabilization measures (pdf)

Congressman Jared Huffman’s Ad Hoc Working group

At the request of several entities, in 2017 Congressman Jared Huffman convened stakeholders in a process referred to as Congressman Jared Huffman’s Potter Valley Project Ad Hoc Committee. The Committee has no formal authority, yet it also has no constraints – thereby enabling constructive dialogue among stakeholders and consideration of a broad range of scenarios for the future of the Potter Valley Project. At the request of Congressman Huffman, PG&E, Sonoma County Water Agency, and California Trout teamed to contract the Consensus Building Institute to provide impartial facilitation of the Ad Hoc Committee. The Ad Hoc Committee offers a promising venue for regional water planning alongside consideration of salmonid population recovery. 

The Ad Hoc Committee identified two key topics that are fundamental to the Potter Valley Project: (1) fish passage above Scott Dam and (2) water supply options. At its January 2018 meeting, the Ad Hoc Committee formed two technical working groups to examine these issues in a focused manner. The Fish Passage and Water Supply Working Groups have examined these issues and reported their findings to the full Ad Hoc Committee for consideration.


The water supply working group convened to address water supply needs and demands across both the Eel and Russian River basins, consider future hydrographs, articulate existing constraints – including costs, maximize benefits of coordinating operations, timing, and flow regimes along with biological considerations for timing, quality, and temperature, and to evaluate a small number potential scenarios that consider fish passage to inform Ad Hoc decision making. This document describes the modeling effort that took place to assess various Project alternatives. Ultimately the only scenario that met Two Basin Solution goals and fish passage needs was scenario two, removal of Scott Dam and a run of the river diversion facility.

The Fish Passage Working Group to identify a prioritized list of conceptual- level fish passage scenarios that would facilitate the ability of migratory fish to reach critical habitats beyond the Potter Valley Project (i.e., above Scott Dam) and promote the recovery and long-term viability of currently depressed populations in the Eel River. To achieve this, the Fish Passage Working Group attempted to identify fish passage alternatives that met the following three objectives: 1. Population viability of Upper Eel River anadromous fishes; 2. Access to abundant high quality habitat; and 3. Functional fish passage.

Executive Summary Fish Passage Evaluation Report (pdf)

Two Basin Partnership – Phase 1

The Two-Basin Partnership was a direct outgrowth of Congressman Huffman’s Ad Hoc process and the group sought to find a solution for the future of the aging Potter Valley Project through a collaborative effort to take over the Project’s license from current owner PG&E. As part of their efforts, the Partners submitted a Notice of Intent to take over the project and completed an Initial Study Report and a Feasibility Study.

The Partners investigated a wide range of potential Project configurations and elements, evaluated costs and benefits of those configurations and elements, and evaluated performance towards their Shared Objectives based on the best available information at the time. The Feasibility Study Report described a potential licensing proposal for the Potter Valley Project. This proposal includes: Regional Entity, Project Plan, Fisheries Restoration Plan, Application Study Plan, and a Finance Plan. While ultimately the Two Basin Partnership’s effort to assume the project license failed, the Feasibility Study Report was supported by a number of technical memos that illustrated the alternatives selection process, provide feasibility level analysis of infrastructure improvements, and assess potential ecosystem and fisheries responses to Project alternatives.

Two Basin Partnership – Phase 2

In early 2022 the Two Basin Partnership abandoned their effort to acquire the Potter Valley Project, saying it could not meet an April 14, 2022 deadline for submitting a license application and that they did not have the money needed to complete all the studies needed to license the project, however, additional studies were completed by the Partnership prior to abandoning their efforts. The studies provide additional refinement of the Feasibility Study on multiple topics, including Scott and Cape Horn Dam removal and the identification of three feasible alternatives to provide an ongoing diversion to meet water users needs and fish passage. 

Two additional, peripheral studies were also completed, one looking at water use and supply options for agricultural interest in Potter Valley and a study identifying a framework for an Eel River wide restoration plan.

  1. Scott Dam and Cape Horn Dam Removal (pdf) – Presents alternatives and feasibility level cost estimates for Cape Horn and Scott dam removal, including estimates for three water supply/fish passage options at Cape Horn dam. 
  2. Coarse Sediment Transport November 2021 (pdf) – Models coarse scale sediment movement following Scott dam removal. 
  3. Eel River Hydraulic Modeling August 2021 (pdf) – Describes the development of a hydraulic model for the Eel River from Scott dam to Dos River and describes application of the model to assess short-term and long-term flooding risk following Scott Dam removal based on results from the sediment transport modeling.
  4. Upper Eel Sediment Supply November 2021 (pdf) – Background study on sediment supply from Dos Rios upstream to Scott dam. 
  5. Cape Horn Dam Fish Passage Improvements (pdf) – Defines fish passage performance criteria, screens alternatives for fish passage and water diversion at Cape Horn dam and develops conceptual designs for feasible alternatives. 
  6. PVID Water Supply Alternatives (pdf) – Includes description of Potter Valley Irrigation District  infrastructure, number of customers, water and land use and provides conceptual design alternatives for PVID water supply. 
  7. Eel Restoration Framework November 2021 (pdf) – Describes a framework for an Eel River fisheries restoration program, develop a scope of work for a restoration and conservation plan.

Mercury Study

One concern with dam removal is the potential for sediments in Lake Pillsbury to contain Mercury. Mercury is naturally occurring throughout much of California’s coast ranges, but can become methylated in anoxic conditions like those found at the bottom of reservoirs. Methylmercury is highly toxic and can bioaccumulate in food webs.

Consultant Geosyntec collected sediment cores from the Lake Pillsbury and Van Arsdale reservoirs to assess the cores for mercury concentrations. The preliminary study indicates that the Lake Pillsbury and Van Arsdale Reservoirs are generally non-contaminated; concentrations of inorganic constituents were consistent with background concentrations of metals in sediments or soils from the Northern California region and organic constituents were found at low level concentrations that are indicative of broad ranging, non-point sources.


In 2022, The Bay Area Council Economic Institute studied the economic benefits of removing both Eel River dams. 

This report seeks to provide an understanding of the economic impacts associated with one likely result of the FERC decommissioning process: that PG&E will remove both Scott and Cape Horn Dams. This outcome is likely due to the reasonable initial capital outlay for PG&E and the minimal long-term operation and maintenance costs associated with dam removal relative to long-term operations and maintenance costs coupled with ongoing state and federal liabilities surrounding fish passage, environmental compliance, and dam safety without a continued revenue source.