Quantification of pre-screen loss of juvenile steelhead in Clifton Court Forebay

California Department of Water Resources (DWR) | August 26th, 2008

Rapid decline of California’s native inland fishes: a status assessment

University of California, Davis (UC Davis) | November 1st, 2010

Degradation of freshwater ecosystems is a global crisis best understood through intensive study of well-studied regional faunas. A quantitative protocol was used

Degradation of freshwater ecosystems is a global crisis best understood through intensive study of well-studied regional faunas. A quantitative protocol was used to determine conservation status of all 129 freshwater fishes native to California. Seven (5%) are extinct; 34 (26%) qualified for listing as endangered or threatened species; 32 (25%) were rated as imperiled, qualifying as California Species of Special Concern, with potential for listing; 34 (26%) rated being on a watch list and 22 (17%) were found to be relatively secure. Of 31 species officially listed under federal and state endangered species acts, 17 (55%) clearly qualified for listing under our criteria and 12 (39%) were rated as species of special concern. Conversely, of 34 extant species with the lowest ratings under our criteria, only 17 (50%) were officially listed. Climate change, area occupied and anthropogenic threats had the largest negative impact on status. Of the 15 categories of anthropogenic threats analyzed, those most likely to diminish status were alien species, agriculture and dams. Overall, 83% of California’s freshwater fishes are extinct, endangered, or in decline, a 16% increase since 1995 and a 21% increase since 1989. The decline seen in California’s inland fishes is probably typical of declines in areas that are less well documented, indicating a strong need for better methods of conservation of freshwater ecosystems.

Reconciling fish and farms: Methods for managing California rice fields as salmon habitat

PLOS | February 24th, 2021

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the pa

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in California’s Central Valley have emerged as ecologically functioning floodplain rearing habitat for juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods to enhance habitat benefits for fall-run Chinook Salmon reared on winter-flooded rice fields in the Yolo Bypass, a modified floodplain managed for flood control, agriculture, and wildlife habitat in the Sacramento River Valley of California. Investigations included studying the effect of 1) post-harvest field substrate; 2) depth refugia; 3) duration of field drainage; and 4) duration of rearing occupancy on in-situ diet, growth and survival of juvenile salmon. Post-harvest substrate treatment had only a small effect on the lower trophic food web and an insignificant effect on growth rates or survival of rearing hatchery-origin, fall-run Chinook Salmon. Similarly, depth refugia, created by trenches dug to various depths, also had an insignificant effect on survival. Rapid field drainage yielded significantly higher survival compared to drainage methods drawn out over longer periods. A mortality of approximately one third was observed in the first week after fish were released in the floodplain. This initial mortality event was followed by high, stable survival rates for the remainder of the 6-week duration of floodplain rearing study. Across years, in-field survival ranged 7.4–61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in California’s recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incremental improvements in design to increase survival. Zooplankton (fish food) in the winter-flooded rice fields were 53-150x more abundant than those sampled concurrently in the adjacent Sacramento River channel. Correspondingly, observed somatic growth rates of juvenile hatchery-sourced fall-run Chinook Salmon stocked in rice fields were two to five times greater than concurrently and previously observed growth rates in the adjacent Sacramento River. The abundance of food resources and exceptionally high growth rates observed.

Record of Decision, Trump Administration Action 5 Operations Plan for the Central Valley and State Water Projects, per Executive Order 14181

U.S. Bureau of Reclamation (USBR) | December 4th, 2025

On January 24, 2025, President Donald J. Trump issued Executive Order 14181 “Emergency Measures To Provide Water Resources In California And Improve Disaster Response I

On January 24, 2025, President Donald J. Trump issued Executive Order 14181 “Emergency Measures To Provide Water Resources In California And Improve Disaster Response In Certain Areas.” A Presidential Memorandum titled “Putting People Over Fish” was signed four days before the Executive Order and references a reliable water supply, but the specific direction to the CVP is found in Executive Order 14181. Section 2 of Executive Order 14181 requires, among other measures, (c) The Secretary of the Interior, including through the Bureau of Reclamation, shall utilize his discretion to operate the CVP to deliver more water and produce additional hydropower, including by increasing storage and conveyance, and jointly operating federal and state facilities, to high­need communities, notwithstanding any contrary State or local laws. The Bureau of Reclamation shall take all available measures to ensure that State agencies — including the California Department of Water Resources — do not interfere with the Bureau of Reclamation’s operation of the project to maximize water delivery to high­need communities or otherwise, including but not limited to the issuance of a new Record of Decision maximizing water deliveries and consistent with the 2020 Record of Decision. Subsection (g) calls for a “proposed plan, for review by the Secretaries, to appropriately suspend, revise, or rescind any regulations or procedures that unduly burden such projects and are not necessary to protect the public interest or otherwise comply with the law.” This ROD implements initial actions in response to Executive Order 14181. Click here for the Reclamation Long Term Operations page,  here for response to the Trump Action 5 gambit from California Department of Water Resources, and here for the response from the State Water Resources Control Board

Recovery plan for Central Valley winter-run chinook salmon, spring-run chinook salmon, and steelhead

National Marine Fisheries Service (NMFS) | July 7th, 2014

Recovery is the process by which listed species and their ecosystems are restored and their future is safeguarded to the point that protections under the Endangered Speci

Recovery is the process by which listed species and their ecosystems are restored and their future is safeguarded to the point that protections under the Endangered Species Act (ESA) are no longer needed. The goal of this Recovery Plan is to recover the endangered Sacramento River winter-run Chinook salmon Evolutionarily Significant Unit (ESU), the threatened Central Valley spring-run Chinook salmon ESU, and the threatened California Central Valley steelhead Distinct Population Segment (DPS). Recovering these species and the Central Valley, San Francisco Bay-Delta Estuary, and Pacific Ocean ecosystems that support them will be challenging and will require shifts in societal values. Californians must work together towards a conservation ethic and practice that ensures wild salmon and steelhead are an important part of coastal California and Central Valley culture for many generations to come.

Recovery Plan for Sacramento-San Joaquin Delta native fishes

U.S. Fish and Wildlife Service (FWS) | November 26th, 1996

Eight fish species are included in the Sacramento-San Joaquin Delta Native Fishes Recovery Plan. The delta smelt is listed as a threatened species. The Sacramento splitta

Eight fish species are included in the Sacramento-San Joaquin Delta Native Fishes Recovery Plan. The delta smelt is listed as a threatened species. The Sacramento splittail (splittail) was proposed as a threatened species on January 6, 1994. This recovery plan will recommend restoration criteria for the splittail that would be appropriate recovery criteria should the species be listed. Longfin smelt, green sturgeon, spring-run, late fall-run, and San Joaquin fall-run chinook salmon are species of concern for which restoration criteria are recommended. Information is also included on Sacramento perch, a species believed to be extirpated from the Delta at this time. Habitat Requirements and Limiting Factors: The eight species included in this recovery plan depend on the Sacramento-San Joaquin Delta for a significant segment of their life history. Threats to the Delta ecosystem and these species include loss of habitat due to increased freshwater exports resulting in increased salinity, loss of shallow-water habitat due to dredging, diking and filling, introduced aquatic species that have disrupted the food chain, and entrainment (movement offish by currents produced by diversions) in State, Federal and private water diversion. State and Federal water projects have also changed the pattern and timing of flows through the Delta. The salmon races are affected by sport and commercial harvest as well as by interactions with hatchery stocks. Recovery and Restoration Objective: Delisting of delta smelt. Restoration of splittail, longfin smelt, green sturgeon, spring-run, late fall-run, San Joaquin fall-run chinook salmon, and Sacramento perch. Recovery and Restoration Criteria: Recovery criteria are quantifiable and species specific and can be used to (1) monitor effectiveness of recovery actions, (2) determine when a species has recovered to a secure level (stabilized), and (3) determine when a species qualifies for delisting. In many cases, criteria are based on two independent measures: population abundance and geographic distribution. For each species a historic base period was established using available data to characterize abundance and distribution during a pre-decline period. The time period over which abundance and distribution criteria must be met was set at five generations. For five of the eight species there is an additional requirement of meeting the criteria through a minimum number of years of stressful environmental conditions. Action Needed: 1. Enhance and restore aquatic and wetland habitat in the Sacramento-San Joaquin River estuary. 2. Reduce effects of commercial and recreational harvest. 3. Reduce effects of introduced aquatic species on Delta native fishes. 4. Change and improve enforcement ofregulatory mechanisms. 5. Conduct monitoring and research on fish biology and management requirements. 6. Assess recovery management actions and re-assess prioritization of actions. 7. Increase public awareness of importance of Delta native fishes.

Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California

U.S. Fish and Wildlife Service (FWS) | September 23rd, 2013

The Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California features five endangered species: two endangered animals, California clapper rail (Rallus

The Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California features five endangered species: two endangered animals, California clapper rail (Rallus longirostris obsoletus) and salt marsh harvest mouse (Reithrodontomys raviventris) and three endangered plants, Cirsium hydrophilum var. hydrophilum (Suisun thistle), Chloropyron molle ssp. molle (soft bird’s-beak), and Suaeda californica (California sea-blite). The biology of these species is at the core of the recovery plan, but the goal of this effort is the comprehensive restoration and management of tidal marsh1 ecosystems. This recovery plan is an expansion and revision of The California Clapper Rail and Salt Marsh Harvest Mouse Recovery Plan (U.S. Fish and Wildlife Service 1984). The historic distribution of the California clapper rail encompasses major tidal marshes between Humboldt Bay and Morro Bay, defining the approximate geographic scope of this recovery plan. In addition to the California clapper rail and the salt marsh harvest mouse, the plan also covers three focal listed plant species that were listed as federally endangered in the 1990s and the northernmost population of an additional plant species. Two of the species, Cirsium hydrophilum var. hydrophilum and Chloropyron molle ssp. molle (this species’ former name is Cordylanthus mollis ssp. mollis which is how it appears on the List of Threatened and Endangered Species, but we use the currently accepted name here), are restricted to the northern reaches of the San Francisco Bay Estuary. The other endangered tidal marsh plant, Suaeda californica, historically occurred in both San Francisco Bay and Morro Bay but, except for three reintroductions to San Francisco Bay, is now restricted to Morro Bay. Another federally listed plant, Chloropyron maritimum ssp. maritimum (salt marsh bird’s-beak; formerly Cordylanthus maritimus ssp. maritimus), has its northern range limit in Morro Bay. Morro Bay was omitted from the Salt Marsh Bird’s-beak Recovery Plan (U.S. Fish and Wildlife Service 1985a) because the taxonomic interpretation at the time classified this population in another subspecies that is not federally listed. Current taxonomic interpretation considers the Morro Bay population as Chloropyron maritimum ssp. maritimum. It is included in this recovery plan due to its co-location with Suaeda californica in Morro Bay. Though recovery strategies and actions are provided for the Morro Bay population of C. maritimum ssp. maritimum, recovery criteria are not, therefore, the species should not be considered covered by the recovery portion of the document. In addition, this recovery plan addresses 11 species or subspecies of concern. These include the salt marsh wandering shrew (Sorex vagrans halicoetes), Suisun shrew (Sorex ornatus sinuosus), San Pablo vole (Microtus californicus sanpabloensis), California black rail (Laterallus jamaicensis coturniculus), three song sparrow subspecies of the San Francisco Bay Estuary (Alameda song sparrow [Melospiza melodia ssp. pusillula], Suisun song sparrow [M.m. maxillaris] and San Pablo song sparrow [M.m. samuelis]), saltmarsh common yellowthroat (Geothlypis trichas sinuosa), old man tiger beetle (Cicindela senilis senilis), Lathryrus jepsonii ssp. jepsonii (delta tule pea), and Spartina foliosa (Pacific cordgrass). These species occur in a variety of tidal marsh habitats where they are limited by the requirements of moisture, salinity, topography, soil types, and climatic conditions. Adjacent uplands and ecotone areas are also crucial habitats for many of these species. Primary threats to all the listed species include historical and current habitat loss and fragmentation due to urban development, agriculture, and diking related to duck hunting; altered hydrology and salinity; non-native invasive species; inadequate regulatory mechanisms; disturbance; contamination; risk of extinction due to small population size; and the most central threat, sea level rise due to climate change.

Relationship of Delta Cross Channel Gate Operations to Loss of Juvenile Winter-run Chinook Salmon at the CVP/SWP Delta Facilities

California Department of Fish and Wildlife (CDFW) | July 1st, 2003

Winter-run Chinook salmon are distinguishable from the three other Chinook runs in the Sacramento River system by the timing of their upstream migration and spawning. Due

Winter-run Chinook salmon are distinguishable from the three other Chinook runs in the Sacramento River system by the timing of their upstream migration and spawning. Due to precipitous decline in the population from the late 1960’s through the late 1980’s, NOAA Fisheries listed the run as “threatened” in August 1989, and subsequently reclassified the run as “endangered” in 1992. The state of California listed the run as endangered in 1989.  Many factors contributed to the decline in the winter-run Chinook population. Among these factors, operation of the federal Central Valley Project and State Water Project has had continuing impacts on winter-run Chinook. Of particular concern have been the direct entrainment losses of juvenile winter-run Chinook at the project export facilities in the Delta. 

Response to the Delta Science Program and Independent Review Panel Report from the 2015 Annual Review of the Long-term Operation Biological Opinions (2015 Annual Review) (January 29, 2016)

Delta Stewardship Council (Delta Council) | January 29th, 2016

Restoring the Heart of a Healthy Estuary: A Review of Restoration in the Sacramento–San Joaquin Delta and Suisun Marsh

Publisher not available | December 19th, 2025

The restoration of native species-dominated ecosystems is critical for improving ecosystem health and meeting policy goals in the Sacramento–San Joaquin Delta and Suisu

The restoration of native species-dominated ecosystems is critical for improving ecosystem health and meeting policy goals in the Sacramento–San Joaquin Delta and Suisun Marsh (upper San Francisco Estuary, collectively), one of the largest estuarine systems in North America. To accomplish large-scale restoration in this heavily altered system, a variety of projects, programs, and motivations inform restoration planning and implementation. Chapter 4 of the Delta Plan synthesizes restoration goals across these efforts to produce comprehensive ecosystem restoration targets of between 60,000 and 80,000 acres across seven ecosystem types by 2050, but a comprehensive review of restoration progress and planning to date is needed. To fill this gap, this paper analyzes the current state of ecosystem restoration in the upper San Francisco Estuary in the context of the Delta Plan targets. We review current scientific and management literature and implementation approaches, and synthesize acreage totals across completed, in-progress, and planned projects for four ecosystem types where substantial development of restoration in the system has occurred: tidal wetland, non-tidal wetland, riparian, and floodplain. We find that tidal wetland restoration has progressed more rapidly than other ecosystem types, motivated by mitigation requirements related to the federal Endangered Species Act. Across all ecosystem types, we identify both promising progress and clear needs for accelerated planning and implementation of restoration projects to meet Delta Plan 2050 targets, and discuss ongoing needs related to science, funding, and implementation.