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  • Title

    Yolo Bypass Salmonid Habitat Restoration and Fish Passage

    Lead California Department of Water Resource [DWR]
    Description The Yolo Bypass Salmonid Habitat Restoration Project works to reconnect the floodplain for fish during the winter season and improve connectivity within the bypass and to the Sacramento River. The project provides seasonal inundation that mimics the natural process of the Yolo Bypass floodplain and improves connectivity within the bypass and to the Sacramento River.
    Science topics Chinook Salmon, Endangered species, Green sturgeon, Habitat restoration, Salmon migration, Salmon rearing, Steelhead Trout, Sturgeon, White Sturgeon
    Updated July 22, 2024
  • Title

    Impact of Urbanization on Chinook Salmon, Steelhead Trout, and Their Prey: a Case Study of the American River

    Lead University of California - Berkeley [UC Berkeley]
    Description The American River provides spawning/rearing habitat for Chinook salmon and steelhead, yet passes through 30 miles of dense urban development. Urban runoff contains pyrethroid insecticides that cause the river to become toxic to standard testing species with every storm event. This study will go beyond observed toxicity, and address toxicity to chironomids, caddisflies, and mayflies, key diet components of juvenile fish in the river. A bioenergetic model will be used to evaluate effects of food web changes on young salmonids. Our key approach is the use of river-side systems with flowing river water that allow us to replicate realistic pesticide exposures, while controlling other variables. We will determine sensitivity to pyrethroids and fipronil of salmonid prey taxa, and expose them, as well as standard testing species, in the flow-through systems through six storm events. We will maintain experimental streams containing riverine benthic invertebrate communities, and measure response to the pyrethroid pulses. To supplement analyses of the indirect, food web-mediated effects, we will measure endocrine effects through vitellogenin induction in salmon and steelhead. Finally, one treatment includes river water from which organic contaminants have been removed by activated charcoal, to help establish cause of toxicity. The goal is to determine if known toxicity in the American River is a threat to benthic invertebrates and, through the food web, to salmon and steelhead.
    Science topics Chinook Salmon, Steelhead Trout, Above highwater refugia, Other discharge contaminants, Food webs
    Updated April 29, 2022
  • Title

    Habitat Values of Native SAV [Submerged Aquatic Vegetation] in the Low Salinity Zone of San Francisco Estuary

    Lead San Francisco State University [SFSU]
    Description We will investigate the importance of native submerged aquatic vegetation (SAV) in providing food web support for native fish species in the low salinity zone of the San Francisco Bay-Delta. These SAV beds, composed primarily of Stuckenia pectinata (sago pondweed), are an extensive feature along many of the islands in Suisun Bay and the west Delta, yet almost nothing is known of their seasonal or interannual patterns, their invertebrate communities, or how their physical structure or food resources influence use by native fishes. We hypothesize that the position of these beds in the shallow subtidal zone along the islands increases habitat options adjacent to wetlands and channels for numerous fish species, including species of concern such as delta smelt and chinook salmon. The objectives of this project are to: 1) characterize patterns in habitat structure, community composition, and productivity of SAV beds in four locations in Suisun Bay and the western Delta over a three year period (with comparisons to non-native Egeria densa beds), 2) document the epifaunal invertebrate community composition and abundance in the Stuckenia beds, 3) assess fish use of these beds through seining and acoustic monitoring of hatchery-tagged fish, 4) utilize stable isotope analyses to evaluate food web relationships within and among the beds, and 5) begin preliminary evaluation of the potential to restore native SAV to subsided lands in this region.
    Science topics Chinook Salmon, Green sturgeon, White Sturgeon, Sacramento Splittail, Delta Smelt, Steelhead Trout
    Updated April 29, 2022
  • Title

    Life History Variation in Steelhead Trout and the Implications for Water Management

    Lead University of California - Santa Cruz [UCSC]
    Description The purpose of this project is to explore the ways in which different stream hydrology and temperature can affect the growth and maturation of steelhead trout. Model examination will incude various stream flow management regimes may affect trout population dynamics region-wide.
    Science topics Steelhead Trout
    Updated April 29, 2022
  • Title

    Synchrony of Native Fish Movements: Synthesis Science Towards Adaptive Water Management in the Central Valley (FishSync)

    Lead University of California - Davis [UC Davis]
    Description Salmon and other native California fishes are in decline and increasingly targeted for enhanced conservation. Acoustic telemetry technologies have emerged, allowing researchers to track fish routes through the Central Valley. Yet while the use of acoustic telemetry has widened, little synthesis has occurred on the large, growing, and expensive datasets that already exist. The main goal of the project is to conduct a synthesis study of existing and high priority telemetry datasets for native and non-native fishes in the Central Valley. Using synchrony of movement rates, through space and time, we will develop a novel behavior-based statistical framework to gain understanding into the environmental conditions that promote movement/passage of diverse native fishes in the Central Valley. The project includes a Technical Advisory Group, composed of members of multiple conservation teams. The group will inform each step of study, strengthen syntheses, and enable rapid communication of results to decision makers. In total, the project will analyze 10 to 15 high-quality telemetry datasets encompassing a range of native fishes and life stages. This synthesis will yield major insights into water management practices that could help improve survival of native fish. (Green sturgeon image is a CDFW photo, taken by Mike Healy. Source: https://californiawaterblog.com/2023/02/12/green-sturgeon-in-california-hidden-lives-revealed-from-long-term-tracking/)
    Science topics Chinook Salmon, Fish, Salmon migration, Steelhead Trout, Sturgeon, White Sturgeon
    Updated March 9, 2026
  • Title

    Delta Regional Monitoring Program

    Lead San Francisco Estuary Institute [SFEI]
    Description The Delta Regional Monitoring Program (RMP) is a stakeholder-directed project formed to develop water quality data necessary for improving our understanding of Delta water quality issues.
    Science topics Hg and methyl mercury, Insecticides, Rodenticides, Herbicides, Fungicides, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Striped bass, Fish
    Updated April 29, 2022
  • Title

    Central Valley Enhanced Acoustic Tagging Project

    Lead National Oceanic and Atmospheric Administration [NOAA]
    Description There is a well documented need for improved detection and associated modeling of salmon migration and survival in the Central Valley. We propose to address this need through an expanded acoustic receiver network and associated real-time and retrospective modeling of the data. The proposed work includes (1) the deployment of real-time receivers that will provide timely information on migrating salmon smolt location and timing, (2) expansion of the existing autonomous acoustic array to increase the coverage and detection efficiency;(3) development of new metrics for the real-time data for key management relevant questions such as entrainment estimates at critical junctions (Georgiana Slough and Delta Cross Channel);and (4) a retrospective analyses directly geared toward improving the quality and robustness of an existing forecasting model - the NMFS enhanced particle tracking model.
    Science topics Chinook Salmon, Steelhead Trout, Green sturgeon
    Updated April 29, 2022
  • Title

    20-mm Survey [Delta Smelt distribution monitoring]

    Lead California Department of Fish and Wildlife [CDFW]
    Description

    California Department of Fish and Wildlife (CDFW) conducts the 20-mm Survey annually to monitor the distribution and relative abundance of larval and juvenile Delta Smelt (Hypomesus transpacificus) in the upper San Francisco Bay Estuary. The survey began in 1995 and supplies near real-time catch data to water and fisheries managers as part of an adaptive management strategy to limit the risk of Delta Smelt entrainment during water exports Data collected: temperature, electro-conductivity, water transparency, turbidity, water volume, tidal stage, fish, and zooplankton.
    Science topics Benthos, Chinook Salmon, Delta Smelt, Green sturgeon, Longfin Smelt, Other zooplankton, Sacramento Splittail, Stage, Steelhead Trout, Tides, Turbidity, Water temperature, White Sturgeon
    Updated March 11, 2026
  • Title

    Fall Midwater Trawl Survey [FMWT]

    Lead California Department of Fish and Wildlife [CDFW]
    Description

    The FMWT was initiated to determine the relative abundance and distribution of age-0 striped bass (Morone saxatilis), delta smelt (Hypomesus transpacificus), longfin smelt (Spirinchus thaleichthys), American shad (Alosa sapidissima), splittail (Pogonichthys macrolepidotus), and threadfin shad (Dorosoma petenense) in the estuary. FMWT has sampled annually since it's inception in 1967, with the exceptions of 1974 and 1979, when sampling was not conducted. The FMWT samples 122 stations each month from September to December and a subset of these data is used to calculate an annual abundance index.

    The FMWT conducts compliance monitoring in collaboration with USBR and DWR to meet permit obligations to the SWRCB (and DRCB) via Water Rights Decisions (D-1485 and D-1641) and USFWS-NMFS biological opinions for Delta Smelt (Hypomesus transpacificus) and salmonids, and for incidental take permits issued by CDFW for operation of the State Water Project (SWP), and the USBR BA/ROD. FMWT also informs Natural Resource Agency Delta Smelt Resiliency Strategy management actions including the Suisun Marsh Salinity Control Gate re-operation and the North Delta Food Web Managed Flow actions. FMWT is used to inform Effects of Outflow Alteration upon Delta Smelt Habitat, Condition, and Survival and Summer-Fall Habitat Action monitoring. 

    Project Objectives
    •    To annually measure the abundance and distribution of selected species of pelagic fishes in the estuary.
    •    To gain understanding of the factors affecting abundance, distribution, and survival of pelagic fishes in the estuary.
    •    To detect introductions of new exotic fish and invertebrates.
    •    Provide baseline data to evaluate management plans and habitat restoration projects. 
    •    To measure availability of fall planktonic food resources.
    Science topics Chinook Salmon, Delta Smelt, Fish, Green sturgeon, Longfin Smelt, Mysis, Other zooplankton, Sacramento Splittail, Stage, Steelhead Trout, Turbidity, Water temperature, White Sturgeon
    Updated February 18, 2026
  • Title

    California Fish Passage Assessment Database [PAD]

    Lead Pacific States Marine Fisheries Commission [PSMFC]
    Description The Passage Assessment Database (PAD) is an ongoing map-based inventory of known and potential barriers to anadromous fish in California, compiled and maintained through a cooperative interagency agreement. The PAD compiles currently available fish passage information from many different sources, allows past and future barrier assessments to be standardized and stored in one place, and enables the analysis of cumulative effects of passage barriers in the context of overall watershed health. The database is set up to capture basic information about each potential barrier. It is designed to be flexible. As the database grows, other modules may be added to increase data detail and complexity.
    Science topics Water operations and exports, Water storage, Water conveyance and infrastructure, Main channels, Chinook Salmon, Steelhead Trout, Water intakes and fish screens and passage
    Updated April 29, 2022
  • Title

    California Natural Diversity Database [CNDDB]

    Lead California Department of Fish and Wildlife [CDFW]
    Description The California Natural Diversity Database (CNDDB) is an inventory of the status and locations of rare plants and animals in California. CNDDB staff work with partners to maintain current lists of rare species, as well as to maintain an ever-growing database of GIS-mapped locations for these species. The CNDDB is a "natural heritage program" and is part of a nationwide network of similar programs overseen by NatureServe (formerly part of The Nature Conservancy). All natural heritage programs provide location and natural history information on special status plants, animals, and natural communities to the public, other agencies, and conservation organizations. The data help drive conservation decisions, aid in the environmental review of projects and land use changes, and provide baseline data helpful in recovering endangered species and for research projects.
    Science topics Mudflats, Intertidal and transition zones, Above highwater refugia, Main channels, Sloughs, Backwater, Submerged aquatic vegetation, Floating aquatic vegetation, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Non forested vegetation, Delta islands, Pacific flyway, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Pelagic fish, Benthos, Salt marsh harvest mouse, Waterfowl, Shorebirds, Gulls, Giant garter snake, California tiger salamander, Insects, Mollusks, Crustaceans, Striped bass, Corbicula and Potamocorbula, Nutria, Water hyacinth, Brazilian waterweed, Spongeplant, Giant reed, Yellow star thistle, Saltwater and freshwater marshes, Habitat, Other species, Fish, Mammals, Birds, Amphibians and reptiles, Invertebrates, Invasive and non native species, Non resident and overwintering birds
    Updated April 29, 2022
  • Title

    Drought Stressor Monitoring

    Lead California Department of Fish and Wildlife [CDFW]
    Description The state of California recently experienced a severe drought and one of the warmest and driest periods of recorded history. The drought lasted for five years, from 2012 to 2016. On January 17, 2014, Governor Jerry Brown declared the drought a state of emergency. This proclamation directed all state agencies to act to prepare for and mitigate drought-related effects on water supply and aquatic species. The California Department of Fish and Wildlife (CDFW) responded by developing and implementing “Drought Stressor Monitoring”. In late 2016 to early 2017, drought conditions improved considerably throughout most of the state when winter storms delivered higher than average levels of rainfall. This report describes the results from a collaborative monitoring effort carried out during the period 2014 to 2017 by scientists from California Department of Fish and Wildlife and other agencies throughout the state.
    Science topics Dissolved oxygen, Chinook Salmon, Steelhead Trout, Fish, Amphibians and reptiles
    Updated April 29, 2022
  • Title

    Middle Sacramento River Salmon and Steelhead Rotary Screw Trap Monitoring (Knights Landing)

    Lead California Department of Fish and Wildlife [CDFW]
    Description

    Description

    The Middle Sacramento River Juvenile Salmon and Steelhead Monitoring Project at Knights Landing operates a monitoring site near the town of Knights Landing (rkm 144), consisting of paired, 8-foot rotary screw traps leashed together and anchored in river. Salmonid emigration data collected at this site provides an early warning of fish emigrating toward the Delta and allows for real-time adaptive management of CVP/SWP water operations. Monitoring begins when water temperatures decrease in the fall allowing for the safe handling of trap captured fish, usually occurring mid to late August, and will continue until the end of June, or until water temperatures increase and safe handling of trap captured fish becomes a concern. Trap catch is counted, identified to species, measured, and weighed. For salmonids specifically, data collection includes enumeration by run, life stage designation, fork length measurement and wet weight for assessing condition of individual fish. 

    Project Need

    Recent updates to the operating criteria of the Central Valley Project, detailed in the 2019 Bureau of Reclamation Biological Assessment (BA) of the Coordinated Long-term Operation of the Central Valley Project (CVP) and State Water Project (SWP), rely on juvenile salmonid monitoring data at Knights Landing to provide an early warning of increased emigration rates of listed salmonids out of the upper Sacramento River. The real-time data provided by the program allow for data related triggers in the operation of the Delta Cross Channel gates. Daily catch data are reported to the Salmon Monitoring Team (SaMT) and are posted on the publicly accessible CalFish website for interested parties. SaMT uses catch data to advise NMFS, through the Water Operations Management Team (WOMT), of entrainment risk in CVP/SWP export facilities, the estimated proportion of juvenile salmonid populations that have entered the Sacramento-San Joaquin Delta and the data driven management triggers detailed in section 4.10.5.3 of the BA; from Oct 1 to Nov 30, if the Knights Landing Catch Index (KLCI) is greater than 3 fish.

    Project Objectives

    • Monitor and report the outmigration of juvenile salmonids from the Sacramento River as they move toward the Sacramento-San Joaquin Delta on a real-time basis
    • Monitor, record and compare movements of emigrating salmonids during specific environmental conditions • Estimate emigrating salmonid numbers and composition in the lower Sacramento River above the Delta
    • Examine the influences of Sacramento River flood relief structures on emigrating juvenile salmonids
    Science topics Chinook Salmon, Steelhead Trout, Surface water flow, Turbidity, Water temperature
    Updated March 26, 2026
  • Title

    Coleman and Livingston Stone Hatchery Releases

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description

    The federal hatcheries mark and tag fish that are released into the river or bay using a combination of coded wire tags (CWT) and adipose fin clipping. The number of fish tagged and the identifiers are reported to the RMPC which is part of the RMIS. The Regional Mark Processing Center (RMPC) provides essential services to international, state, federal, and tribal fisheries organizations involved in marking anadromous salmonids throughout the Pacific region. These services include regional coordination of some tagging and fin marking programs, maintenance of databases for Coded Wire Tag Releases, Recoveries, and Locations, as well as the dissemination of reports of these data in electronic or printed form when requested. These databases are known collectively as the Regional Mark Information System (RMIS).
    Science topics Chinook Salmon, Conductivity, Dissolved oxygen, pH, Steelhead Trout, Turbidity, Water temperature
    Updated June 26, 2025
  • Title

    Bioaccumulation Monitoring Program

    Lead San Francisco Estuary Institute [SFEI]
    Description The Bioaccumulation Oversight Group (BOG) is a subcommittee of the SWAMP Roundtable that provides oversight of SWAMP's statewide bioaccumulation monitoring program. The BOG is also a workgroup of the California Water Quality Monitoring Council, and in this role manages the Safe to Eat Portal and is a forum for coordination of bioaccumulation monitoring in California. The mission of the BOG is to assess the impacts of contaminants in fish and shellfish on beneficial uses in California water bodies through statewide monitoring under SWAMP and perform syntheses of information from other studies, and to develop an internet portal that presents this information to decision-makers and the public in a form that they can easily use. See the Workgroup Charter for more information.
    Science topics Fishing, Main channels, Sloughs, Backwater, Chinook Salmon, Steelhead Trout, Pelagic fish, Striped bass
    Updated April 29, 2022
  • Title

    Central Valley Angler Survey

    Lead California Department of Fish and Wildlife [CDFW]
    Description CDFW uses a stratified sampling design to interview anglers and check catches in the Delta and throughout the Sacramento system. Focus of the program is on salmonids, but they also record striped bass and sturgeon data, as available.
    Science topics Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Fish
    Updated April 29, 2022
  • Title

    Mokelumne River Fish Hatchery

    Lead East Bay Municipal Utilities District
    Description The Mokelumne River supports Central Valley fall-run Chinook salmon (Oncorhynchus tshawytscha) (fall-run), which is the only salmon run known to naturally occur in this waterway (Clark 1929). Fall-run are listed as a Species of Concern under the federal Endangered Species Act (NMFS 2004). Camanche Dam, which impounds Camanche Reservoir is the upper limit of anadromous fish migration in the Mokelumne River. East Bay Municipal Utility District (EBMUD) initiated construction of Camanche Reservoir in 1963. As mitigation for blocking access to spawning grounds for salmonids, EBMUD provided funding for the original construction of the MOK in 1964.The MOK is located on the south bank of the Mokelumne River at the base of Camanche Dam. While EBMUD provides funding for fall-run production, the California Department of Fish and Wildlife (CDFW) administers and operates the hatchery. The Commercial Salmon Stamp Fund provided funding for an additional MOK building built in 2002 and continues to financially support the MOK. On an annual basis the MOK produces fall-run for mitigation (Mitigation Element) and for ocean salmon enhancement (Ocean Enhancement Element). The annual MOK production goal is 6,400,000 fall-run smolts (3,400,000 for Mitigation Element and 3,000,000 for Ocean Enhancement Element). The hatchery operations are involved with tagging and monitoring fish to assess the success of the hatchery program.
    Science topics Surface water flow, Salinity, Water temperature, Dissolved oxygen, pH, Main channels, Chinook Salmon, Steelhead Trout
    Updated April 29, 2022
  • Title

    Mokelumne River Rotary Screw Trap Monitoring

    Lead East Bay Municipal Utilities District
    Description EBMUD operates 2-3 RSTs downstream of the Mokelumne Fish Hatchery.
    Science topics Surface water flow, Water temperature, Dissolved oxygen, pH, Turbidity, Main channels, Chinook Salmon, Steelhead Trout, Sacramento Splittail, Striped bass, Fish, Water intakes and fish screens and passage
    Updated April 29, 2022
  • Title

    Juvenile Salmonid Monitoring - Red Bluff Diversion Dam

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description The Red Bluff Fish and Wildlife Office (RBFWO) established a juvenile fish monitoring program using rotary-screw traps at the Red Bluff Diversion Dam (RBDD) in 1994. The primary objectives of this project at present are to (1) obtain juvenile winter Chinook production indices and to correlate these indices with estimated escapement from adult estimates provided by the winter Chinook carcass survey, (2) define seasonal and temporal patterns of abundance of winter, spring, fall and late-fall run Chinook salmon and steelhead trout passing RBDD and (3) obtain relative abundance information (catch per unit volume) for green sturgeon and lamprey to monitor trends in abundance.
    Science topics Water conveyance and infrastructure, Surface water flow, Stage, Velocity, Water temperature, Turbidity, Chinook Salmon, Steelhead Trout, Green sturgeon, Water intakes and fish screens and passage
    Updated April 29, 2022
  • Title

    San Francisco Bay Study

    Lead California Department of Fish and Wildlife [CDFW]
    Description

    The San Francisco Bay Study (Bay Study) was established in 1980 to determine the effects of freshwater outflow on the abundance and distribution of fish and mobile crustaceans in the San Francisco Estuary, primarily downstream of the Sacramento-San Joaquin Delta. Sampling ranges from south of the Dumbarton Bridge in South San Francisco Bay, to just west of Alcatraz Island in Central San Francisco Bay, throughout San Pablo and Suisun bays, north to the confluence Steamboat and Cache sloughs on the Sacramento River, and east to Old River Flats on the San Joaquin River. The open water or boat survey samples 52 stations monthly: 35 original stations, 7 stations added in 1988, 4 stations added in 1991, and 6 stations added in 1994. The study included a beach seine survey, discontinued in 1987, and a shore-based ringnet survey for crabs, discontinued in 1994. The Bay Study uses a 42-foot stern trawler to sample with 2 trawl nets at each open water station. The otter trawl, which samples demersal fishes, shrimp, and crabs, is towed against the current at a standard engine rpm for 5 minutes then retrieved. The midwater trawl, which samples pelagic fishes, is towed with the current at a standard engine rpm for 12 minutes and retrieved obliquely such that all depths are sampled equally. The open water survey included a plankton net that sampled larval fish and crustaceans, but this was discontinued in 1989. Fish, caridean shrimp, and brachyuran crabs are identified, measured, and counted. Shrimp and crabs are also sexed. Sampling effort is quantified (i.e. distance towed, volume of water filtered) and salinity, water temperature, Secchi depth, and station depth are measured;wave height, tide, cloud cover, and tow direction are categorized. The length, catch, and effort data is used to calculate catch-per-unit-effort (CPUE) by species and age class. The CPUE data is used to calculate monthly and annual abundance indices, which are used to track seasonal and annual population trends. Important factors that control or regulate abundance and distribution of fish and mobile crustaceans in the estuary include salinity, temperature, freshwater outflow, ocean temperature, upwelling, and surface currents, primary and secondary productivity, and introduced species. We are interested in how species respond to changes in the physical environment on several temporal scales - seasonal, annual, decadal, and longer. We produce several annual Status and Trends reports that summarize recent changes for the most commonly collected species. These reports are published in the Spring issue of the IEP Newsletter, which can be found at http://iep.water.ca.gov/report/newsletter. 
    Science topics Chinook Salmon, Conductivity, Crustaceans, Delta Smelt, Green sturgeon, Longfin Smelt, Mammals, Sacramento Splittail, Steelhead Trout, Water temperature, White Sturgeon
    Updated March 12, 2026
  • Title

    Anadromous Fish Abundance and Trends

    Lead Pacific States Marine Fisheries Commission [PSMFC]
    Description In 1998, the Pacific States Marine Fisheries Commission, the California Department of Fish and Game, and the National Marine Fisheries Service began a cooperative effort to collect, archive, and enter into standardized database formats the information generated by fisheries resources agencies throughout California. Data for this project have been collected from a variety of government sources, such as the Department of Fish and Game and the US Forest Service, and non-government sources, such as tribal fisheries monitoring, university research, local watershed stewardship programs, and numerous additional fisheries stakeholders. The database contains a significant amount of information regarding the current and historic status of California's anadromous fish. The building and expansion of the cooperative anadromous fisheries abundance dataset is largely dependent on funding, support, and sharing the vision that this type of program in California is imperative. The wealth of this type of information that has already been compiled into the CalFish database demonstrates what can be accomplished through interagency cooperation.
    Science topics Main channels, Sloughs, Backwater, Seasonally flooded, Open water, Chinook Salmon, Steelhead Trout, Habitat, Fish
    Updated April 29, 2022
  • Title

    Anadromous Fish Distribution

    Lead California Department of Fish and Wildlife [CDFW]
    Description To meet the need for consistent statewide anadromous distribution data, CalFish cooperators have initiated a series of projects to begin pulling existing distribution data together for select anadromous species. We began developing Coho Distribution in 2002, published the first publicly available version in July 2007 and most recently updated with new information in June 2012. We extended this effort to Steelhead in the Fall of 2004, first published the data in the Fall of 2007 and updated it in Fall 2009 and most recently June 2012. Additionally, we are seeking funding to further extend this effort to Chinook in the very near future.
    Science topics Fishing, Main channels, Sloughs, Backwater, Chinook Salmon, Steelhead Trout
    Updated April 29, 2022
  • Title

    Smelt Larva Survey

    Lead California Department of Fish and Wildlife [CDFW]
    Description

    The Smelt Larva Survey (SLS), initiated in January 2009, provides near real-time distribution data for Longfin Smelt larvae in the Delta, Suisun Bay and Suisun Marsh for the protection of larval and juvenile Longfin Smelt from December through March.

    Project Need

    The data obtained from SLS are used by agency managers to assess vulnerability of Longfin Smelt and Delta Smelt larvae to entrainment in south Delta export pumps. This larval fish survey is designed to provide a more comprehensive coverage of distribution and abundance of larval Longfin Smelt and Delta Smelt in the upper estuary, and augment other sources of data used in the decision-making process for water operations, including the existing IEP 20-mm Survey field operations when the two programs overlap temporally. This survey is also a requirement of Section 5.2 of Incidental Take Permit No. 2081-2019-066-003 for the State Water Project, issued by CDFW under the authority of the California Endangered Species Act and pursuant to Fish and Game Code sections 2081(b) and 2081(c), and California Code of Regulations, Title 14. Export and flow management are guided through distribution and catch criteria based on this study.

    Project Objectives

    • Determine the larval Longfin Smelt and Delta Smelt abundance, temporal and spatial distribution in near real time.
    • Determine whether the temporal and spatial distribution and abundance of larval and post-larval Longfin Smelt and Delta Smelt are determinate factors on the level of entrainment losses.

    Schedule of Milestones

    • Every two weeks from December to March field surveys will be conducted and field and laboratory results will be reported weekly to the Smelt Monitoring Team (SMT) and the WOMT team starting 5 days after the field sampling are concluded. Shortly afterwards, raw and calculated data will be uploaded to the Region 3’s SLS Survey web page.
    • By the end of the calendar year a draft survey summary article will be submitted to the Editor of the IEP newsletter for publication.
    Science topics Chinook Salmon, Conductivity, Delta Smelt, Green sturgeon, Longfin Smelt, Main channels, Sacramento Splittail, Salinity, Sloughs, Stage, Steelhead Trout, Turbidity, Water temperature, White Sturgeon
    Updated April 8, 2026
  • Title

    Spring Kodiak Trawl Survey

    Lead California Department of Fish and Wildlife [CDFW]
    Description The Spring Kodiak Trawl Survey (SKT) has sampled annually since its inception in 2002. The SKT determines the relative abundance and distribution of spawning delta smelt (Hypomesus transpacificus). The SKT samples 40 stations each month from January to May. These 40 stations range from San Pablo Bay upstream to Stockton on the San Joaquin River, Walnut Grove on the Sacramento River, and the Sacramento Deep Water Ship Channel. Each 'Delta-wide' survey takes approximately 4 - 5 days per month to complete. Historically, 'Delta-wide' surveys were followed by a 'Supplemental' survey two weeks later to intensively sample areas of highest delta smelt concentration to estimate the proportion of male and female delta smelt that were in pre-spawning, spawning and spent maturation stages. Beginning in 2008, in an effort to minimize take of spawning adults, routine 'Supplemental' surveys were discontinued and are now only conducted under the recommendation of the Smelt Working Group and the approval of managers.
    Science topics Stage, Salinity, Water temperature, Turbidity, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Conductivity, Other species
    Updated April 29, 2022
  • Title

    Summer Townet Survey

    Lead California Department of Fish and Wildlife [CDFW]
    Description

    The Summer Townet Survey (STN) is a long-term effort to monitor young pelagic fishes in the upper San Francisco Estuary. Since 1959, STN has sampled locations from eastern San Pablo Bay to Rio Vista on the Sacramento River, and to Stockton on the San Joaquin River; and a single station in the lower Napa River. The study area was expanded in 2011 to include the Sacramento Deep Water Ship Chanel and Cache Slough. Currently, 40 stations are sampled as a survey every other week June through August for a total of 6 surveys. Fish sampling uses a conical, fixed-frame net, which is pulled obliquely through the water column 2 to 3 times at each station. Data collected at 31 stations are used to calculate annual relative abundance indices for age-0 Striped Bass (Morone saxatilis) and Delta Smelt (Hypomesus transpacificus). The remaining 8 stations are sampled to increase our understanding of juvenile fish abundance and distribution in the lower Napa River and the north Delta. Starting in 2005, a zooplankton net was added to assess fish food resources at each station and a subset of the fish collected are retained for diet analysis by CDFW researchers. Zooplankton sampling informs several management actions focused on Delta Smelt habitat improvements including collections of additional zooplankton samples for the Suisun Marsh Salinity Control Gate re-operation. Finally, the STN also measures environmental variables including water temperature, water clarity and specific conductivity. Managers and researchers use data collected by STN to inform decisions and improve and understand the health of the upper San Francisco Estuary.
    Science topics Chinook Salmon, Delta Smelt, Fish, Green sturgeon, Longfin Smelt, Main channels, Mysis, Other zooplankton, Sacramento Splittail, Sloughs, Steelhead Trout, Striped bass, White Sturgeon, Zooplankton
    Updated February 18, 2026
  • Title

    Delta Juvenile Fish Monitoring Program [DJFMP]

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description

    The Delta Juvenile Fish Monitoring Program (DJFMP) has monitored natural-origin and hatchery-origin juvenile Chinook Salmon (Oncorhynchus tshawytscha) and other fish species within the San Francisco Estuary (SFE) since 1976 using a combination of midwater trawls and beach seines. Since 2000, three trawl sites and at least 58 beach seine sites have been sampled weekly or biweekly within the SFE and lower Sacramento and San Joaquin Rivers. The main objectives of the DJFMP are:
    1. Document the long-term abundance and distribution of juvenile Chinook Salmon in the Delta.
    2. Comprehensively monitor throughout the year to document the presence of all races of juvenile Chinook Salmon.
    3. Intensively monitor juvenile Chinook salmon during the fall and winter months for use in managing water project operations (Delta Cross Channel gates and water export levels) on a real-time basis.
    4. Document the abundance and distribution of Steelhead.
    5. Document the abundance and distribution of non-salmonid species.

     
    Science topics Aquatic vegetation, Chinook Salmon, Conductivity, Crustaceans, Dissolved oxygen, Endangered species, Environmental drivers, Estuaries, Fish, Habitat, Historical ecology, Intertidal and transition zones, Invasive and non native species, Invertebrates, Jellyfish, Main channels, Monitoring methods and techniques, Mysis, Open water, Other species, Pelagic fish, Salinity, Salmon migration, Salmon rearing, SAV and FAV, Steelhead Trout, Turbidity, Water conveyance and infrastructure, Water management, Water operations and exports, Water temperature
    Updated May 21, 2025
  • Title

    Suisun Marsh Fish Study

    Lead University of California - Davis [UC Davis]
    Description The University of California, Davis has been involved in fish and wildlife monitoring and research within Suisun Marsh for 35 years and has been instrumental in detecting important trends associated with naturally fluctuating environmental conditions as well as anthropogenic influences. Research has included a 35+ year time series on the fish and invertebrate communities of the slough networks, research on waterfowl nesting patterns and population biology, and research on the demography of salt marsh harvest mouse. The Suisun Marsh Fish Study anchors this effort as it is the longest established survey in Suisun marsh. It will continue the research of Professor Peter Moyle under the direction of John Durand, and will focus upon the detection of changes in the aquatic ecosystem in response to developing stressors in the San Francisco Estuary (SFE). This time series is designed to further our understanding of the ecology and function of the fish community residing within Suisun Marsh and the San Francisco Estuary (SFE), and acts as one of the key surveys with Interagency Ecological Program's monitoring effort.
    Science topics Stage, Tides, Salinity, Water temperature, Dissolved oxygen, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Pelagic fish, Benthos, Salt marsh harvest mouse, Mollusks, Crustaceans, Striped bass, Corbicula and Potamocorbula, Conductivity, Environmental drivers, Other species, Fish, Invertebrates
    Updated April 29, 2022
  • Title

    Fish Salvage and Genetic Analysis

    Lead U.S. Bureau of Reclamation [USBR]
    Description The State Water Project (SWP), operated by the California Department of Water Resources (DWR), and the Central Valley Project (CVP), operated by the U.S. Bureau of Reclamation, export water out of the San Francisco Bay Delta for urban and agricultural use in California. Salvage of fish at both facilities is conducted 24 hours a day, seven days a week at regular intervals. Since 1957, the U.S. Bureau of Reclamation (USBR) has salvaged fish at the Tracy Fish Collection Facility (TFCF). CDFW's Fish Facilities Unit, in cooperation with DWR, began salvaging fish at the Skinner Delta Fish Protective Facility (SDFPF) in 1968. Fish salvage and loss rates are used to determine the need for changes in operations in response to National Marine Fisheries Service (NMFS) regulatory requirements. Salvage and loss monitoring includes daily monitoring and reporting of estimated loss of salvaged fish, as well as monitoring and reporting of salvaged Coded Wired Tagged (CWT) hatchery fish. This information is widely used by West Coast fisheries agencies to collect information on natural and hatchery-reared stocks of salmon and steelhead. Our state-of-the-art genetic analysis techniques are used to quantify salvage rates of listed runs of California's Central Valley juvenile Chinook Salmon. We also utilize advanced genetic analysis techniques to identify different populations of Central Valley juvenile Chinook Salmon, and actively participate in development of new analysis methods.
    Science topics Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Striped bass, Fish, Invasive and non native species
    Updated April 29, 2022
  • Title

    Feather River Hatchery/ Oroville Facility Fishery Studies

    Lead California Department of Water Resource [DWR]
    Description DWR conducts Feather River fishery studies to estimate adult abundance for both spring-run and fall-run Chinook salmon, and to conduct tagging studies using young fish from Feather River Hatchery. Our program has expanded in recent years and also supports additional fishery studies commissioned for the Oroville Facilities relicensing through the Federal Energy Regulatory Commission. The Feather River Fish Hatchery is a joint operation between CDFW and DWR. Generally, CDFW is responsible for raising and releasing the fish. DWR operates the fish traps and analyzes the data for returns and populations. According to their website, of the 5 hatcheries (Feather, Coleman, Nimbus and ??) Feather accounts for most ocean catch. The hatchery also monitors and reports returning adults (https://nrm.dfg.ca.gov/documents/ContextDocs.aspx?cat=Fisheries--FishProductionDistribution&sub=Anadromous_Fish_Trap_Counts)
    Science topics Chinook Salmon, Steelhead Trout
    Updated April 29, 2022
  • Title

    Recreational Freshwater Fishing Licenses

    Lead California Department of Fish and Wildlife [CDFW]
    Description California tracks the number of fishing licenses sold each year, by county.
    Science topics Fishing, Chinook Salmon, Steelhead Trout, Green sturgeon, Pelagic fish, Fish
    Updated April 29, 2022
  • Title

    Yolo Bypass Fish Monitoring

    Lead California Department of Water Resource [DWR]
    Description California Department of Water Resources (DWR) has operated a fisheries monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: (1) collect baseline data on lower trophic levels (phytoplankton, zooplankton, and aquatic insects), juvenile fish and adult fish, hydrology, and water quality parameters;(2) investigation of the temporal and seasonal patterns in chlorophyll-a concentrations, including whether high concentrations are exported from the Bypass during agricultural and natural flow events and the possibility of manipulating bypass flows to benefit listed species like Delta Smelt (Hypomesus transpacificus) and Chinook salmon (Oncorhynchus tshawytscha). The YBFMP operates a rotary screw trap and fyke trap, and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts.
    Science topics Chinook Salmon, Chlorophyll A B, Conductivity, Delta Smelt, Direction, Dissolved oxygen, Endangered species, Fish, Flood, Food webs, Green sturgeon, Habitat, Habitat restoration, Insects, Intertidal and transition zones, Invasive and non native species, Invertebrates, Longfin Smelt, Main channels, Nitrogen, Nitrogen and ammonia, Nutrients, Other species, Other zooplankton, Pelagic fish, pH, Phytoplankton, Primary production, Sacramento Splittail, Salmon migration, Salmon rearing, Saltwater and freshwater marshes, SAV and FAV, Seasonally flooded, Solar irradiance, Stage, Steelhead Trout, Striped bass, Sturgeon, Submerged aquatic vegetation, Surface water flow, Tides, Turbidity, Velocity, Water, Water temperature, Wetlands, White Sturgeon, Zooplankton
    Updated August 28, 2024
  • Title

    Fish Restoration Program Monitoring

    Lead California Department of Fish and Wildlife [CDFW]
    Description

    Description
    The CDFW Fish Restoration Program will collect fish and invertebrate data near existing and planned tidal wetlands. These data will provide information on how fish and invertebrate communities change pre-/post-restoration. While collecting these data, the variability of invertebrate catches will be assessed for each gear type to determine the optimal number of samples per sampling site.
    Need
    Under the 2008 and 2019 State Water Project/Central Valley Project Joint Operations Biological Opinion from United States Fish and Wildlife Service, 2009 and 2019 National Marine Fisheries Service, and 2009 and 2020 State Water Project Incidental Take Permit, Department of Water Resources (DWR) is required to restore >8,000 acres of tidal wetlands in the Sacramento-San Joaquin Delta (Delta) and Suisun Marsh to improve habitat and food web resources for threatened fishes. The Fish Restoration Program is responsible for biological monitoring in these restored tidal habitats to assess their success for providing habitat and food web benefits for at-risk native fishes.
    Project Objectives

    • Assess the food web resources (nutrients, phytoplankton, zooplankton, and macroinvertebrates) associated with pre- and post-restoration tidal wetlands, as well as with existing reference wetlands
    • Assess the fish community of restoring wetlands - use by rearing salmonids and characterization the predator and competitor communities
    • Determine the level of spatial and temporal replication necessary to make sampling design recommendations for long-term monitoring, and develop newer methods for wetland restoration
    • Synthesize existing data on submersed aquatic vegetation in these sites to refine our sampling procedures.
    Science topics Carbon, Chinook Salmon, Chlorophyll A B, Crustaceans, Delta Smelt, Dissolved oxygen, Green sturgeon, Insects, Invertebrates, Longfin Smelt, Mollusks, Nitrogen and ammonia, Other zooplankton, pH, Phosphorous, Phytoplankton, Sacramento Splittail, Salinity, Steelhead Trout, Submerged aquatic vegetation, Turbidity, Water temperature, White Sturgeon
    Updated April 8, 2026
  • Title

    Non-Invasive Environmental DNA Monitoring to Support Tidal Wetland Restoration

    Lead University of California - Davis [UC Davis]
    Description In this project we use single-species and multi-species environmental DNA (eDNA) approaches to monitor tidal wetland restoration sites and paired reference sites (existing, unrestored tidal wetlands located near restoration sites) in the San Francisco Bay Delta (SFBD). We are working in coordination with the CDFW Fish Restoration Program (FRP) and other collaborators so our eDNA detections can be paired with physical detections of fishes from their trawling efforts. Ultra-sensitive DNA single species detection methods are being used to identify restoration site use by listed species (Delta Smelt, Longfin Smelt, winter- and spring-run Chinook Salmon) while the DNA metabarcoding approach will evaluate entire fish communities (groups of different fish species) at restored and reference sites. Aside from revealing restored habitat use by other fishes, metabarcoding will reveal potential ecological interactions between Endangered Species Act listed and non-listed species, through concurrent detection in time and space. Sampling throughout the year will allow us to identify seasonal trends in fish use of restored and reference sites. This project will demonstrate the utility of eDNA detection as a non-invasive (no take), cost-effective monitoring tool that can complement conventional surveys of restored tidal wetlands in the SFBD. Our results can be incorporated into an adaptive monitoring framework for tidal wetland restoration, to increase success of future restoration projects.
    Science topics Chinook Salmon, Delta Smelt, Endangered species, Estuaries, Fish, Green sturgeon, Habitat, Habitat restoration, Invasive and non native species, Invertebrates, Longfin Smelt, Mollusks, Pelagic fish, Restoration, Restoration planning, Sacramento Splittail, Salmon migration, Salmon rearing, Steelhead Trout, Striped bass, Sturgeon, Tidal wetlands, Wetlands, White Sturgeon
    Updated May 24, 2024
  • Title

    Open-Source Resources for the Sacramento-San Joaquin Delta Telemetry Research Community

    Lead Cramer Fish Sciences
    Description There is a great deal of telemetry data amassed from studies in the Sacramento-San Joaquin Delta. It continues to grow every year with special studies and monitoring efforts. Multiple research priorities surrounding fish ecology in the Delta could be addressed, at least in part, by synthesizing the myriad telemetry data sets that exist; this work would benefit greatly from the centralization and standardization of data workflows surrounding telemetry research. With the guidance of a PIT Advisory Team, we plan to establish a collection of open-source, technology-agnostic, accessible resources to support a reproducible and transparent telemetry data workflow for researchers in the region. The workflow and resources do not invent new procedures, rather improve and standardize those already used by the telemetry research community. This will bring us in closer alignment with centralized, coordinated data workflows that have been successfully implemented in other regions and data communities. The final open-source set of resources will include a design and roadmap for implementing a central telemetry database and workflow, an R package for the preparation, QA/QC, and basic analysis of telemetry data, and a regional workshop offering training programs in the proposed telemetry data workflow.
    Science topics Chinook Salmon, Fish, Other species, Salmon migration, Steelhead Trout, Striped bass, Sturgeon
    Updated August 26, 2024
  • Title

    Standard Operating Procedure for Diagnosing and Addressing Predator Detections in Salmon Telemetry Data

    Lead University of Washington [UW]
    Description Tag predation is a complicating factor in juvenile salmon telemetry studies that can bias results, delay timely reporting, and prevent effective data synthesis. This project addresses the problem by (1) characterizing predatory fish movement patterns from existing telemetry data in the Delta; (2) developing a standard operating procedure for diagnosing and handling detections of predated tags in salmon telemetry studies; and (3) implementing the recommendations in a software package in Program R that includes code, a “library” of expected predator behaviors, and example vignettes. The R package will be freely available for download at www.cbr.washington.edu.
    Science topics Chinook Salmon, Endangered species, Fish, Intertidal and transition zones, Invasive and non native species, Predation, Salmon migration, Steelhead Trout, Striped bass
    Updated April 30, 2025
  • Title

    Development and maintenance of SacPAS website and research for management of Central Valley salmon and other fish species

    Lead University of Washington [UW]
    Description

    SacPAS serves to provide information integration services to the Central Valley Project Improvement Act and practitioners working on matters related to ESA-listed fishes. The web-based services relate fish passage to environmental conditions and provide resources for evaluating the effects of river management and environmental conditions on salmon passage and survival.

    The work performed as part of this agreement includes developing, maintaining, and making accessible query tools and decision support tools to access: historical, real-time and forecasted data; data summaries and visualizations; and hindcasts, forecasts, and scenario-derived predictions from statistical and mechanistic models. More specifically, the objectives are to: 

    1)    Maintain and extend a secondary data repository of historical, real-time, and forecasted fish, environmental, and operational data from the Sacramento River and other river systems in the Central Valley, integrated from primary, public databases. 

    2)    Maintain and improve the data query and visualization tools and services provided through the SacPAS website (https://www.cbr.washington.edu/sacramento/) for historical, real-time, and forecasted environmental and fish data.

    3)    Conduct research and provide access to modeling tools for fish survival and migration, through the SacPAS website, in support of Reclamation-funded and ESA-mandated activities, especially in efforts to predict, track, and evaluate the efficacy of proposed or actual actions.
     
    Science topics Chinook Salmon, Delta Smelt, Endangered species, Environmental drivers, Fish, Flows, Green sturgeon, Longfin Smelt, Salmon migration, Stage, Steelhead Trout, Sturgeon, Temperature, Velocity, Water, Water intakes and fish screens and passage, Water management, Water operations and exports, Water storage, Water temperature, White Sturgeon
    Updated March 8, 2026
  • Title

    Fish and Fish Habitat Monitoring - Wetland Regional Monitoring Program.

    Lead University of California - Davis [UC Davis]
    Description

    The Wetland Regional Monitoring Program (WRMP) Fish and Fish Habitat Monitoring project is a collaborative effort to track biological responses to tidal wetland restoration in the San Francisco Estuary. Monthly sampling is conducted across a network of benchmark, reference, and project restoration sites in the South Bay and North Bay, with the goal of evaluating how wetland restoration influences fish assemblages, habitat use, and ecological condition.

    The study uses primarily otter trawls to monitor fish and macroinvertebrate communities. Standardized field methods align with those used in long-term monitoring programs to ensure comparability and data integration across regions. Environmental data, including water temperature, salinity, and dissolved oxygen, are collected in tandem with biological sampling to assess habitat quality and seasonal dynamics.

    The program addresses WRMP Guiding Question #4: How do policies, programs, and projects to protect and restore tidal marshes affect the distribution, abundance, and health of fish and wildlife? The data support adaptive management, regulatory compliance, and science-based restoration planning by identifying key habitats, tracking restoration performance, and detecting regional patterns in species composition and abundance over time.
    Science topics Backwater, Benthic, Benthos, Biosentinels, Bivalve, Corbicula and Potamocorbula, Crustaceans, Dissolved oxygen, Dredging, Drought, Endangered species, Environmental drivers, Estuaries, Fish, Flows, Habitat, Habitat restoration, Intertidal and transition zones, Invasive and non native species, Invertebrates, Jellyfish, Longfin Smelt, Marsh wildlife, Mollusks, Monitoring methods and techniques, Mudflats, Mysis, Nature-based solutions, Other species, Pelagic fish, pH, Resilience, Restoration, Restoration planning, Sacramento Splittail, Salinity, Sloughs, Steelhead Trout, Striped bass, Sturgeon, Tidal wetlands, Tides, Turbidity, Wastewater discharge, Water, Water temperature, Wetland mapping, Wetlands, White Sturgeon
    Updated January 29, 2026
  • Title

    Mossdale Spring Trawl

    Lead California Department of Fish and Wildlife [CDFW]
    Description

    Description

    The Mossdale Trawl occurs two miles downstream of Mossdale Landing County Park (river miles 56), and upstream of the Old River confluence. Timing and production (indices and estimates) for the out-migrating fall-run Chinook salmon smolts has been monitored at this location since 1987. Additionally this trawl captures coded wire tagged Chinook smolts and is the primary capture site for these fish being used to estimate survival of Chinook smolts in the river system. Results from this project, therefore document information on the out-migration timing, survival, and the magnitude of nonmarked smolt production from the San Joaquin Basin passing into the South Delta. The trawl also captures steelhead outmigrants and provides an index of these outmigrants for the entire San Joaquin River Basin.

    Project Need

    This project needs to identify annual juvenile Chinook salmon production in the San Joaquin River Basin. This project provides data supporting water management in the San Joaquin River basin and the Delta. Enumerating steelhead (Oncorhynchus mykiss) migrating through the San Joaquin River into the south Delta. Developing method to differentiate fall and spring run juvenile Chinook salmon migrating in the San Joaquin River basin.

    Project Objectives

    • What is the annual juvenile Chinook salmon production in the San Joaquin River Basin?
    • How do water quantity and quality conditions affect smolt production trends?
    • How many Oncorhynchus mykiss passage at Mossdale trawl?
    Science topics Steelhead Trout
    Updated March 25, 2026