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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

    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

    Improving Green Sturgeon Population and Migration Monitoring

    Lead University of California - Santa Cruz [UCSC]
    Description Green sturgeon is a listed species under the federal Endangered Species Act. This project supports the recovery and management of the southern distinct population segment of green sturgeon by improving population and migration monitoring. Improved monitoring is recommended in multiple initiatives to help protect this species, such as the Green Sturgeon Recovery Plan. There is some uncertainty on whether the most appropriate green sturgeon monitoring techniques are being used. This project compares the different estimation and monitoring techniques to identify the superior protocol. To compare the effectiveness of different techniques, scientists will monitor green sturgeon in the Sacramento River using sonar technology. Monitoring data will be used to estimate the population size and death rates due to by-catch. This project will also review and synthesize past acoustic telemetry data to determine if the data can be modeled to improve population size estimates.
    Science topics Green sturgeon
    Updated June 3, 2024
  • 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 Stage, Tides, Other zooplankton, Water temperature, Turbidity, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Benthos
    Updated April 29, 2022
  • 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

    Lower Sacramento River Green Sturgeon Telemetry Monitoring

    Lead California Department of Fish and Wildlife [CDFW]
    Description To better understand emigration, California Department of Fish and Wildlife is undertaking a collaborative effort with University of California Davis Biotelemetry Laboratory to capture and acoustically tag 100 green sturgeons and 100 white sturgeons per year for three years. CDFW staff conducted sampling by deploying and tending 33-m variable mesh gill nets anchored with 18-kg pyramid weights. Juvenile sturgeon are surgically implanted with Vemco® V9 69 kHz acoustic transmitters and released near the point of capture. An array of Vemco® acoustic receivers deployed throughout the SFBDE collect detection data for acoustically tagged juvenile sturgeons. To date, (January 2018) CDFW and UCD staff tagged 16 juvenile green sturgeon and 11 juvenile white sturgeon over 159 days of sampling effort.
    Science topics Green sturgeon, White Sturgeon
    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

    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

    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. The 1999 IEP Technical Report, "Report on the 1980-1995 Fish, Shrimp, and Crab Sampling in the San Francisco Estuary, California", is a good source of basic information. This report is out-of-print, but can be found at www.water.ca.gov/iep/docs/tech_rpts/tech_rprt_63_toc.html. website: https://water.ca.gov/-/media/DWR-Website/Web-Pages/Programs/Environmental-Services/Interagency-Ecological-Program/Files/2019-IEP-Work-Plan_2018-12-11.pdf?la=en&hash=C305D1B1DA7931D95E8676247669F098F26A28FA
    Science topics Water temperature, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Crustaceans, Conductivity, Mammals
    Updated April 29, 2022
  • Title

    Smelt Larva Survey

    Lead California State Water Resources Control Board [SWRCB]
    Description The Smelt Larva Survey provides near real-time distribution data for longfin smelt larvae in the Delta, Suisun Bay and Suisun Marsh. Sampling takes place within the first two weeks in January and repeats every other week through the second week in March. Each 4-day survey consists of a single 10-minute oblique tow conducted at each of the 35 survey locations (see map) using an egg and larva net. The 505-micron mesh net is hung on a rigid frame shaped like an inverted-U, which in turn is attached to skis to prevent it from digging into the bottom when deployed. The net mouth area measures 0.37 m2. The conical net tapers back from the frame 3.35 m to a 1-liter cod-end jar, which collects and concentrates the sample. Immediately after each tow, juvenile fishes are removed, identified, measured and returned to the water immediately, and the remaining larvae are preserved in 10% formalin for later identification in the Lab in Stockton.
    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
    Updated April 29, 2022
  • 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

    Sturgeon Study

    Lead California Department of Water Resource [DWR]
    Description Staff of the Sturgeon Study make estimates of sturgeon abundance, relative abundance, harvest rate, and survival rate by using data from Commercial Passenger Fishing Vessels (Party Boats;CPFV), various creel surveys, and a mark-recapture program. We monitor the relative abundance of sturgeon by calculating catch per unit effort (CPUE) from data submitted by Commercial Passenger Fishing Vessels. The Department's Marine Region compiles the data, we request the data at intervals, and we calculate CPUE. By applying tags to sturgeon and monitoring the subsequent ratio of tagged fish to untagged fish, we calculate sturgeon abundance, relative abundance, harvest rate, and survival rate. During August-October we use nets in San Pablo Bay and/or Suisun Bay to collect sturgeon, then we tag and release them on-site. Each tag includes our mailing address and a unique code, and some tags include a reward value. By posting "Tagged-fish Wanted" posters around the Estuary and making presentations, we encourage anglers to return tags to us. We also recover tags by talking with anglers during various creel surveys.
    Science topics Main channels, Green sturgeon, White Sturgeon, Habitat
    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

    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

    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 The Fish Restoration Program (FRP), an inter-agency agreement between the California Department of Fish and Wildlife (CDFW) and the California Department of Water Resources (DWR), will restore at least 8,000 acres of tidal wetlands in the Sacramento-San Joaquin Delta (Delta) and Suisun Marsh pursuant to requirements in federal Biological Opinions and the California Incidental Take Permit for operation of the State Water Project and Central Valley Project. The rationale for restoration is that state or federally listed fish species, Delta Smelt Hypomesus transpacificus, spring-run and winter-run Central Valley Chinook Salmon Oncorhynchus tshawytscha, and Longfin Smelt Spirinchus thaleichthys will benefit from increased availability of habitat and food web resources. The CDFW FRP Monitoring Team is responsible for monitoring the biological effectiveness of individual FRP tidal wetland restoration projects. Fish catch, invertebrate catch, and water quality data have been collected as baseline monitoring data and to determine the most efficient methods for monitoring wetland restoration efforts.
    Science topics Nitrogen and ammonia, Phosphorous, Carbon, Chlorophyll A B, Phytoplankton, Other zooplankton, Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Submerged aquatic vegetation, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Insects, Mollusks, Crustaceans, Invertebrates
    Updated April 29, 2022
  • 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

    The value of information is context dependent: a demonstration of decision tools to address multi-species river temperature management under uncertainty

    Lead CALFED Bay-Delta Program
    Description

    Tradeoffs among objectives in natural resource management can be exacerbated in altered ecosystems and when there is uncertainty in predicted management outcomes. Multicriteria decision analysis (MCDA) and value of information (VOI) are underutilized decision tools that can assist fisheries managers in handling tradeoffs and evaluating the importance of uncertainty. We demonstrate the use of these tools using a case study in the Sacramento River, California, U.S.A., where two imperiled species with different temperature requirements, winter-run Chinook Salmon (Oncorhynchus tshawytscha) and Green Sturgeon (Acipenser medirostris), spawn and rear in the artificially cold Shasta Dam tailwater. A temperature-control device installed on Shasta Dam maintains cool water for Chinook Salmon; however, uncertainties exist related to the effects of temperatures on the spawning and rearing of both species. We consider four alternative hypotheses in models of early life-stage dynamics to evaluate the effects of alternative temperature-management strategies on Chinook Salmon and Green Sturgeon management objectives. We used VOI to quantify the increase in management performance that can be expected by resolving hypothesis-based uncertainties as a function of the weight assigned to species-specific objectives. We found the decision was hindered by uncertainty; the best performing alternative depends on which hypothesis is true, with warmer or cooler alternative management strategies recommended when weights favor Green Sturgeon or Chinook Salmon objectives, respectively. The value of reducing uncertainty was highest when Green Sturgeon was slightly favored, highlighting the interaction between scientific uncertainty and decision makers' values. Our demonstration features MCDA and VOI as transparent, deliberative tools that can assist fisheries managers in confronting value conflicts, prioritizing resolution of uncertainty, and optimally managing aquatic ecosystems.

    Science topics Chinook Salmon, Fish, Flows, Green sturgeon, Salmon rearing, Sturgeon, Temperature, Water conveyance and infrastructure, Water temperature
    Updated November 12, 2025
  • Title

    Analyzing flow regime effects on adult green sturgeon migration in Central California rivers: Science and policy

    Lead University of California - Davis [UC Davis]
    Description

    The Sacramento River and its tributaries serve as critical habitat for the green sturgeon, listed as federally threatened due to its declining population and the impacts of anthropogenic activities such as dam operations and water extraction. We currently lack an understanding of the relationship between flow regimes and sturgeon migration, which is essential for developing effective management strategies to support the species' conservation and for required analysis under state and federal law. By modeling this relationship, this project will contribute to more informed water management, leading to fewer litigation risks for agencies and better outcomes for sturgeon.

    This project will model the effects of flow regimes on adult Southern Distinct Population Segment (sDPS) green sturgeon migration within the Sacramento River basin to enhance sturgeon conservation and water management. Specifically, the research will model how flows and temperature affect adult green sturgeon spawning migration. The model will be used to forecast sturgeon movements under various flow scenarios, and the model, the results, and an explanation of their significance will be widely distributed via a website (with a publicly accessible modeling app), a policy brief, a public workshop, and other outreach.

    Science topics Flows, Green sturgeon
    Updated February 6, 2026
  • 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 25, 2025