Historically, millions of salmon returned to California’s rivers each year. Today, those numbers have plummeted to a fraction of their former levels, with hatcheries now playing a vital role in sustaining the remaining populations. A decade of severe drought, punctuated by sporadic rain and snow events, has further worsened the challenges facing salmon.
The California Salmon Strategy, introduced in January 2024, is a state-led initiative aimed at combating the alarming decline in salmon populations, which has been driven by factors such as drought and climate change. The strategy outlines key priorities and actions to support the restoration of these iconic fish.
At the June meeting of the California Water Commission, Sheena Holley, Salmon Strategy Implementation Coordinator for the Department of Fish and Wildlife; Marc Commandatore, Statewide Restoration Initiatives Branch Manager at the Department of Water Resources; and Erik Ekdahl, Chief Deputy Director at the Water Board, provided Commissioners with an update on the progress of the salmon strategy’s implementation.
California’s Salmon Diversity
California is home to four major species of salmon: chinook, coho, pink, and chum. Among these, chinook and coho dominate the state’s waterways. Chinook salmon are particularly remarkable due to their four genetically distinct run times, which align with the seasons when adults return to freshwater to spawn. For example, spring-run chinook make their journey back to rivers in the spring.
Salmon play a critical role in maintaining healthy ecosystems. They provide a vital food source for numerous species and enrich habitats by transporting nutrients from the ocean to freshwater systems.
Despite their ecological importance, California’s salmon populations are in steep decline. This year marked the third consecutive closure of the commercial fall-run salmon fisheries, with only limited recreational harvests permitted. These closures reflect the dire state of salmon populations, which are being pushed to the brink by poor river and ocean conditions, climate change, and habitat degradation.
The situation is especially critical for spring-run and winter-run chinook salmon, both of which are listed as threatened or endangered at the state and federal levels. These populations face moderate to high extinction risks due to their small numbers and fragile demographics.
“The Sacramento River winter run is a particularly important salmon run because they exhibit a life history strategy found nowhere else on the West Coast,” explained Sheena Holley, Salmon Strategy Implementation Coordinator for the Department of Fish and Wildlife. “They’re unique in that they can spawn in summer months when air and water temperatures are at their highest on the Sacramento River. Winter-run are currently limited to one spawning reach below the Shasta Dam that is highly dependent on cold water releases during the summer. There is also a large-scale reintroduction program ongoing on Battle Creek, following barrier removal on the North Fork.”
Spring-run chinook are also in peril, with two consecutive years of cohort failure—a devastating blow for a species with a three-year life cycle. “Cohort failure means either adult returns were very low, or river conditions during outmigration were so poor that few juveniles survived,” Ms. Holley noted. “Two years of cohort failure can be really devastating.”
California salmon strategy for a hotter, drier future
The Salmon Strategy identifies six key priorities essential to salmon recovery: removing barriers and modernizing infrastructure for salmon migration; restoring and expanding habitat for spawning and rearing; protecting water flows and quality in key rivers at critical times; modernizing salmon hatcheries; transforming technology and management systems for climate adaptability; and strengthening partnerships.
Within these six priorities, there are 71 specific actions, each with timelines and benchmarks set for completion by the end of Governor Newsom’s term in 2026. These actions form the foundation of salmon recovery efforts, with firm deadlines designed to drive implementation and progress.
As of March 2025, a progress report released by the California Natural Resources Agency (CNRA) showed that 7% of the projects were in the planning stages, 67% were in progress, and 26% had been completed.
The speakers provided updates on the state’s progress across all six priorities.
Priority 1: Remove Barriers and Modernize Infrastructure for Salmon Migration
In California, dams and other in-water infrastructure have significantly hindered salmon migration, affecting both upstream spawning and downstream juvenile migration. These barriers block approximately 90% of historical spawning and rearing habitats, particularly in higher elevation streams. This loss is especially concerning given the downstream impacts of climate change.
While some dams can be modernized to improve fish passage, others have become obsolete and are being removed. On the Feather and Yuba rivers, notable progress has been made toward reintroducing spring-run Chinook salmon, with pilot studies led by the California Department of Fish and Wildlife (CDFW) and the Department of Water Resources (DWR). On both rivers, eggs collected from the Feather River Fish Hatchery have been deposited in gravel beds. On the Yuba River, juveniles are being captured and released downstream of passage barriers to inform future reintroduction strategies.
“For the Feather River, this marks the first time spring-run Chinook salmon have been above Oroville Dam since its construction in 1968, and for the Yuba River, this is the first time spring-run salmon have been in the upper watershed since Englebright Dam was built in 1941,” said Ms. Holley.
Efforts are also underway on the South Fork Battle Creek, where a memorandum of understanding (MOU) has been signed by state and federal fish agencies, Reclamation, and PG&E to advance infrastructure removal projects. These efforts aim to restore volitional passage at remaining facilities. This work is critical, as winter-run Chinook salmon are currently confined to spawning reaches below Shasta Dam and a few restoration areas in the North Fork Battle Creek. Expanding access to additional habitat in Battle Creek not only increases spawning opportunities but also provides a safeguard against climate change and population collapse.
“This project is particularly significant because Battle Creek is one of the few tributaries that support all four runs of Chinook salmon. Restoring habitat here will benefit all runs,” said Ms. Holley.
In October 2024, the removal of four dams on the Klamath River was completed, opening up approximately 420 miles of newly accessible habitat. The results are already promising: fall-run Chinook salmon have migrated to Shovel Creek and Spenser Creek, and as of late April, the Fall Creek Hatchery has produced around 244,000 Chinook salmon and 36,000 coho salmon.
“This project serves as a cornerstone of the salmon recovery strategy, completed both on time and within budget,” said Ms. Holley. “Although we’ve reached the end of the dam removal phase, we’re just beginning the recovery process. A reintroduction and restoration monitoring plan is now in place to evaluate these efforts and guide future recovery initiatives.”
Priority 2: Restore and Expand Habitat for Salmon Spawning and Rearing
The restoration efforts in California are struggling to keep pace with the growing threats to its biodiversity, particularly the challenges facing salmon populations. A significant portion of the state’s wetlands has been lost, and many major rivers are no longer connected to their natural floodplains. These wetlands and floodplains are critical ecosystems, as they serve as food-rich environments. Research shows that when salmon spend more time in reconnected floodplains, they grow larger before migrating to the Pacific Ocean. Larger, healthier salmon are more likely to survive their journey to the ocean and successfully return to their spawning grounds.
To accelerate restoration efforts, the Cutting the Green Tape initiative has streamlined the review and approval process for restoration projects. The California Department of Fish and Wildlife (CDFW) has reduced the average permitting time from several months to just 48 days and introduced a single application for restoration projects. Through this initiative, CDFW has permitted 50 salmon restoration projects, enhancing over 640 miles of stream.
The Salmon Habitat Restoration Prioritization Initiative (SHARP), a partnership between NOAA Fisheries and CDFW, focuses on identifying and implementing priority actions to restore salmon and steelhead habitats. Action plans are currently in development, with $30 million allocated to habitat restoration projects. Additional efforts include nature-based solutions, such as wetland restoration for flood protection and beaver translocation to improve spawning and rearing habitats.
In September 2024, the levee at Lookout Slough was breached, marking the completion of the largest tidal wetland restoration project ever undertaken in the Delta, spanning 3,400 acres. The project included constructing over three miles of a 25-foot-tall setback levee to enhance flood protection for nearby communities, excavating 26 miles of open tidal channels, and restoring native habitat through grading, fill placement, and natural revegetation.
The Dutch Slough project in the south-central Delta has added another 1,200 acres of tidal floodplain habitat, complete with public trails.
“So with Lookout Slough and Dutch Slough, we’ve added almost 5,000 acres of habitat that didn’t exist before,” said Marc Commandatore. “These are new projects that have come online in the last couple of years as part of the strategy.”
More habitat projects are on the horizon. In October 2024, state and federal agencies signed the Floodplain Forward Memorandum of Understanding (MOU), supported by the Floodplain Forward Coalition, which includes landowners, irrigation districts, and conservation organizations. This agreement strengthens state-federal collaboration in planning, designing, and implementing multi-benefit floodplain projects within the Sacramento River Basin. These projects aim to enhance flood protection, restore habitats and ecosystems, improve groundwater recharge and water supply reliability, and support farming and managed wetland operations.
Priority 3: Protect Water Flows and Water Quality in Key Rivers at the Right Times to Support Salmon
Habitat restoration alone cannot ensure the survival of salmon without sufficient cold stream flows. Without adequate cold water, juvenile salmon are unable to complete their life cycle, making it impossible to grow their populations.
To address this, the California Department of Fish and Wildlife (CDFW), through a multi-partner environmental flows framework, has developed new tools to establish instream flow metrics. These metrics are provided to the State Water Board to guide water management decisions. CDFW has completed instream flow analyses on four streams identified in the 2014 California Water Action Plan, as well as eight additional streams.
To improve coordination between federal and state-operated water projects, the Department of Water Resources (DWR) and the Bureau of Reclamation reinitiated consultation on water operations in 2021. This collaboration resulted in several significant milestones in 2024. In November, CDFW issued a new Incidental Take Permit for the State Water Project’s operations, while the U.S. Fish and Wildlife Service and the National Marine Fisheries Service (NMFS) issued biological opinions in November and December, respectively, for the joint operations of the State Water Project and the Central Valley Project.
Both the incidental take permit and the biological opinions will use science and adaptive management to help make informed decisions on water operations in key salmon waterways,” said Ms. Holley. The NMFS Biological Opinion included improved Shasta Reservoir operations on the upper Sacramento River, which take into account carryover water storage and enhance temperature management for winter-run spawning and egg incubation downstream of Shasta.
Water Board actions to support the strategy
The Water Board plays an important role in salmon recovery by utilizing its regulatory authority to develop permits, policies, and procedures that aim to protect and enhance the salmon population.
Erik Ekdahl highlighted that only the Russian River, under a biological opinion requiring specific seasonal flows, has a dedicated regulatory instream flow. Elsewhere, limited stream segments tied to dam operations have bypass requirements, but these differ from minimum or dedicated instream flows that extend the full length of a river.
Emergency instream flow regulations have been implemented during critical droughts for the Scott and Shasta Rivers, as well as Mill, Deer, and Antelope Creeks in the Sacramento River watershed. However, Ekdahl acknowledged the challenges of establishing dedicated instream flows. “There’s a huge data and understanding gap—why are instream flows important, and how do we translate that into specific goals, benchmarks, and actions?” he said.
One initiative calls for the State Water Board to complete supply-demand assessment pilot projects in three watersheds. These projects aim to link water diversion data from the Cal WTRS system to water availability, helping inform local water management. While Ekdahl admitted the data isn’t perfect, he emphasized it’s a critical first step toward creating accurate, timely, and actionable datasets.
Ekdahl also provided an update on the long-overdue Bay Delta Water Quality Control Plan. Objectives for the San Joaquin tributaries were updated in 2018, while work on the Sacramento and Delta tributaries continues. A draft plan was released in October 2024, with public comments closing in January 2025. The Board is now reviewing feedback, with an updated plan expected soon, followed by additional public comment and workshops.
Priority 4: Modernize Salmon Hatcheries
The California Department of Fish and Wildlife (CDFW) operates 22 hatcheries across the state, some of which date back to the early 1900s. To modernize these facilities, CDFW released its first comprehensive climate resiliency assessment for state-owned and operated hatcheries. The assessment outlines strategies to enhance water supply, improve water quality, and optimize rearing operations, thereby better adapting to changing environmental conditions.
As part of the Klamath dam removal project, CDFW transitioned hatchery production from Iron Gate to the upgraded Fall Creek Hatchery. The plan is to operate this facility for less than 10 years, allowing for the gradual reintroduction of fish into the Klamath River Basin following the removal of the dams.
In December 2024, construction was completed on the Salmon Conservation and Research Facility (SCAR) on the San Joaquin River. This facility is dedicated to promoting genetic diversity to support the reintroduction of spring-run salmon, which were extirpated from the river in the 1940s.
Hatchery operations are also evolving with increased production and adaptive release strategies. This year, CDFW increased fall-run production to over 27.5 million fish to support salmon fisheries and rebuild Sacramento River fall-run populations. Additionally, CDFW and the U.S. Fish and Wildlife Service are piloting fry release projects, releasing fish at smaller sizes and earlier in the year when river conditions are more favorable.
Advancements in science are transforming hatchery practices. Parental-based tagging now allows scientists to take tissue samples from spawning pairs and create genetic tags for their offspring. These tags enable researchers to identify whether fish are of hatchery or natural origin, as well as gather data on age, run, release date, and location.
In April, parental-based tagging confirmed the presence of a male salmon from the McCloud River reintroduction efforts at the Livingston Stone Hatchery on the Sacramento River. “This is a significant milestone in tracking and understanding the success of reintroduction efforts,” said a CDFW representative.
Priority 5: Transform Technology and Management Systems for Climate Adaptability
Protecting salmon demands innovative technology and real-time data to drive informed decision-making. To enhance coordination and strategy, the California Department of Fish and Wildlife (CDFW) has established a Salmon Executive Steering Committee. This committee meets monthly to review progress on the state’s salmon strategy and address other priority actions for salmon conservation.
CDFW is also leveraging advanced data assessment tools and modernizing salmon abundance forecasting and harvest models to improve resource management. These updates aim to provide more accurate predictions and support sustainable fisheries.
In parallel, the Bureau of Reclamation has developed an advanced water temperature modeling platform. This platform features enhanced temperature models for Shasta, Folsom, and New Melones reservoirs, enabling more effective management of cold water releases to support salmon and other native fish species. These efforts represent a critical step forward in safeguarding salmon populations and their habitats.
Priority 6: Strengthen partnerships
Building and strengthening partnerships is essential for advancing research and fostering collaboration to ensure the long-term survival of salmon. The California Department of Fish and Wildlife (CDFW) has partnered with the Cal Poly Humboldt USGS Cooperative Research Unit to support post-removal monitoring of the Klamath dams. This includes using advanced technology, such as underwater sonar, to count fish returns. The research unit is also assisting in the development of a juvenile salmon predictive mortality model to better understand mortality caused by pathogens, including C. shasta, which leads to intestinal hemorrhaging and necrosis.
CDFW is also working closely with tribal nations and federal partners on the reintroduction of salmon and steelhead upstream of the former Klamath dams. In 2023, a co-management agreement was established between CDFW and the Winnemem Wintu Tribe to reintroduce winter-run salmon above Shasta Dam. These agreements recognize tribes as equal decision-making partners and commit to incorporating traditional ecological knowledge and tribal cultural values into restoration and reintroduction efforts.
This year, 80,000 winter-run salmon eggs will be placed in a 26-mile stretch of the McCloud River, a habitat they haven’t occupied since 1945. A collection system will capture the young fish as they outmigrate, transporting them around Shasta Dam and releasing them into the main stem of the Sacramento River.
“This is a pilot study, so we’re going to learn from it and figure out where we can go in the future,” said Marc Commandatore. “The partnership is strong. It’s taken some hits recently with the challenges of the federal government, but our partners are still there, still meeting with us, and will continue for another field season.”
