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Title	Physiological Mechanisms of Environmental tolerance in Delta Smelt [Hypomesus transpacificus]: From Molecules to Adverse Outcomes
Lead	University of California - Davis [UC Davis]
Description	The proposed project directly addresses priority research detailed by the Delta Science Program to protect native fishes that depend on the Bay-Delta system focusing on adaptations to local habitats and physiological tolerances to key environmental stressors;in delta smelt (Hypomesus transpacificus). Temperature and salinity changes associated with anthropogenic climate change are likely to further exacerbate delta smelt population declines. We hypothesize that delta smelt tolerance to forecasted temperature rises and salinity intrusions into the Bay-Delta system can be assessed at a mechanistic level, and that acclimation thresholds can be established by means of genomic responses. This proposal builds upon successful development of a cDNA microarray for delta smelt containing approximately 2000 individual gene fragments, and the subsequent application of biomarkers for assessing the effects of chemical stressors on larval development with links to swimming behavior. We propose to develop a Next Generation oligonucleotide microarray in delta smelt, with ca. 15K genes, in order to assess mechanistic tolerance to changes in gemperature and salinity. Genomic studies will be conducted integrating effects on energetic activity and swimming performance studies, in an interdisciplinary approach that will permit the establishment of links between tolerance mechanisms and adverse outcomes.
Science topics	Delta Smelt, Water temperature, Salinity, Turbidity
Updated	April 29, 2022

Title	San Francisco Bay Joint Venture
Lead	U.S. Fish and Wildlife Service [USFWS]
Description	The San Francisco Bay Joint Venture (SFBJV) brings together over one hundred environmental organizations, governmental agencies, landowners, and the business community to achieve a common goal and vision: protect, restore and enhance wetlands throughout the nine Bay Area counties, for the benefit of wildlife and people. The San Francisco Bay Joint Venture (SFBJV) is one of twenty-two habitat-based Migratory Bird Joint Ventures (JV) that cover nearly all of the U.S. and Canada and much of Mexico. The SFBJV coordinates strategic habitat conservation throughout the nine San Francisco (SF) Bay Area counties in accordance with the SFBJV Implementation Plan. SFBJV partners work to protect, restore and enhance habitats through project implementation and by advancing related science, policy and communication priorities. The Joint Venture program provides opportunities to develop and deliver creative solutions to our current conservation challenges through the power of collaboration and partnership. The SFBJV is funded by the U.S. Fish and Wildlife Service (USFWS) and grants from other partners and programs.
Science topics	Hunting, Agriculture, Urban development, Recreation and tourism, Surface water flow, Flood, 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, Delta islands, Pacific flyway, Waterfowl, Shorebirds, Gulls, Saltwater and freshwater marshes, Habitat, Non resident and overwintering birds
Updated	April 29, 2022

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	Pacific Flyway Shorebird Survey
Lead	Point Blue Conservation Science
Description	PFSS is a coordinated multi-partner monitoring program led by Point Blue Conservation Science designed to guide the management and conservation of wintering shorebirds in the Pacific Flyway. The PFSS contributes data to the Migratory Shorebird Project, the largest coordinated survey of wintering shorebirds on the Pacific Coast of the Americas spanning 10 countries from Canada to Peru.
Science topics	Hunting, Flood, Mudflats, Intertidal and transition zones, Above highwater refugia, Sloughs, Submerged aquatic vegetation, Floating aquatic vegetation, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Non forested vegetation, Delta islands, Pacific flyway, Shorebirds, Saltwater and freshwater marshes, Habitat, Non resident and overwintering birds
Updated	April 29, 2022

Title	The Heron and Egret Project
Lead	Audubon Canyon Ranch
Description	Our current work focuses on the effects of climate change and human disturbance to heronries.
Science topics	Intertidal and transition zones, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Waterfowl, Shorebirds, Saltwater and freshwater marshes
Updated	April 29, 2022

Title	Audubon Christmas Bird Count [CBC]
Lead	National Audubon Society
Description	Each November, birders interesting in participating in the CBC can sign up and join in through the Audubon website. From December 14 through January 5 each year tens of thousands of volunteers throughout the Americas brave snow, wind, or rain, and take part in the effort.
Science topics	Mudflats, Intertidal and transition zones, Above highwater refugia, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Non forested vegetation, Delta islands, Pacific flyway, Waterfowl, Shorebirds, Gulls, Saltwater and freshwater marshes, Habitat, Non resident and overwintering birds
Updated	April 29, 2022

Title	California Partners In Flight [CalPIF]
Lead	Point Blue Conservation Science
Description	The CalPIF mission is to promote the conservation of resident and migratory landbirds and their habitats in California through research, monitoring, education, and collaboration among public and private landowners and managers, government agencies, non-government organizations, and individuals and other bird conservation efforts. The California chapter of Partners in Flight (CalPIF) was established in 1992. The California Partners in Flight program has completed eight habitat and bioregion based Bird Conservation Plans (BCP's) for Riparian, Oak Woodlands, Coastal Scrub and Chaparral, Grasslands, Coniferous Forests, Sagebrush, Desert, and the Sierra Nevada Bioregion. These BCPs are for every land manager and researcher interested in improving habitat for landbirds. These plans are dynamic documents that will follow a continous process of developing and updating conservation recommendations for California's habitats based on the latest scientific monitoring and research data.
Science topics	Mudflats, Intertidal and transition zones, Above highwater refugia, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Non forested vegetation, Delta islands, Pacific flyway, Waterfowl, Shorebirds, Gulls, Non resident and overwintering birds
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	North American Breeding Bird Survey [BBS]
Lead	U.S. Geological Survey [USGS]
Description	The North American Breeding Bird Survey (BBS) is the primary source for critical quantitative data to evaluate the status of continental bird species, keeping common birds common and helping fuel a $75 billion wildlife watching industry.
Science topics	Mudflats, Intertidal and transition zones, Above highwater refugia, Main channels, Sloughs, Backwater, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Non forested vegetation, Delta islands, Pacific flyway, Waterfowl, Shorebirds, Gulls, Saltwater and freshwater marshes, Habitat, Birds, Non resident and overwintering birds
Updated	April 29, 2022

Title	Marine Invasive Species Program [MISP]
Lead	California Department of Fish and Wildlife [CDFW]
Description	The Marine Invasive Species Program (MISP) is responsible for analysis of shipping vectors (pathways) responsible for the introduction of non-indigenous species (NIS) into California's coastal waters. MISP has partnered with the Smithsonian Environmental Research Center (SERC) and Moss Landing Marine Laboratories (MLML) to undertake an extensive program to analyze spatial and temporal patterns of NIS invasions in marine and estuarine waters of California. MISP collaborates with the California State Lands Commission (CSLC) to regulate and minimize the introduction of Nonindigenous Species (NIS) into California by ocean-going vessels. MISP is partners with the Smithsonian Environmental Research Center (SERC) to conduct biological surveys monitoring the coastal waters of California to determine the level of invasion by NIS;and San Jose State University's Moss Landing Marine Labs (MLML) to conduct genetic analysis of NIS. The California Ballast Water Management Act of 1999 initiated baseline surveys by the California Department of Fish and Wildlife (CDFW) to document the distribution of nonindigenous species in the state's coastal and estuarine waters.
Science topics	Striped bass, Corbicula and Potamocorbula, Water hyacinth, Brazilian waterweed, Spongeplant, Giant reed, Yellow star thistle, Invasive and non native species
Updated	April 29, 2022

Title	Monitoring Avian Productivity and Survivorship
Lead	The Institute for Bird Populations
Description	The MAPS Program is a continent-wide collaborative effort among public agencies, non-governmental groups, and individuals to assist the conservation of birds and their habitats through demographic monitoring. Since 1989, more than 1,200 MAPS stations spread across nearly every state and Canadian province have collected more than 2 million bird capture records.
Science topics	Mudflats, Intertidal and transition zones, Above highwater refugia, Main channels, Sloughs, Backwater, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Non forested vegetation, Delta islands, Pacific flyway, Waterfowl, Shorebirds, Gulls, Saltwater and freshwater marshes, Habitat, Birds, Non resident and overwintering birds
Updated	April 29, 2022

Title	eBird
Lead	Cornell University - Lab of Ornithology
Description	eBird is the world's largest biodiversity-related citizen science project, with more than 100 million bird sightings contributed each year by eBirders around the world. A collaborative enterprise with hundreds of partner organizations, thousands of regional experts, and hundreds of thousands of users, eBird is managed by the Cornell Lab of Ornithology.
Science topics	Mudflats, Intertidal and transition zones, Above highwater refugia, Main channels, Sloughs, Backwater, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Forests, Non forested vegetation, Delta islands, Pacific flyway, Waterfowl, Shorebirds, Gulls, Saltwater and freshwater marshes, Habitat, Birds, Non resident and overwintering birds
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	Aquatic Invasive Species Programs
Lead	California Department of Parks and Recreation [PARKS]
Description	The Aquatic Weed Control Program includes both floating and submersed aquatic vegetation. DBW uses an Integrated Pest Management strategy with the following components: - Public information and education - Prevention - Pre-established action levels for chemical, biological and physical control - Environmental monitoring Since submersed and floating aquatic vegetation are well established in the Sacramento- San Joaquin Delta, eradication may not be feasible, while controlling invasive growth is likely to lessen negative economic and biological impacts.
Science topics	Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Main channels, Sloughs, Backwater, Floating aquatic vegetation, Water hyacinth, Brazilian waterweed, Spongeplant, Conductivity, Saltwater and freshwater marshes, Other species
Updated	April 29, 2022

Title	Benthic Organism Study
Lead	U.S. Bureau of Reclamation [USBR]
Description	This program operates under the Interagency Ecological Program's (IEP) Environmental Monitoring Program (EMP). "The Benthic Organism monitoring effort was started in 1975 and currently monitors 10 sites across the estuary's salinity gradient, from Suisun Bay upstream to Clifton Court Forebay and Stockton, on a monthly basis. Benthic invertebrates are collected with a PONAR grab, preserved, identified, and enumerated. In addition to mandated monthly monitoring of benthic invertebrates, we also conducted special studies of benthic invertebrates using spatial intensive sampling schemes. These special studies complement the long-running mandated monitoring and provide a more comprehensive picture of the benthic community of the Upper San Francisco Estuary." Changes in benthic fauna presence, abundance and distribution associates physical factors are measured in the estuary to evaluate the impacts of water project operations. 426 species in 10 phyla have been collected to date. Data is also used to detect introduced species. Sediment composition data also collected to document general trends at sites where benthic organisms are collected. https://emp.baydeltalive.com/projects/12727/page
Science topics	Suspended sediment, Bedload, Deposition, Erosion, Insects, Mollusks, Crustaceans
Updated	April 29, 2022

Title	Endangered Species Project
Lead	California Department of Pesticide Regulation [DPR]
Description	In California, DPR has been studying endangered species protection issues with federal funding since 1988. DPR activities include mapping sites occupied by federally listed species, evaluating pesticide exposure risks to inhabited sites, classifying risk and developing protection strategies to minimize risk as needed. There are currently 359 federally listed species in California including federally protected endangered and threatened species, proposed endangered, proposed threatened and Category 1 candidate species (that await only administrative processes to become protected species). Collectively, the federally listed species may occupy about 16 million acres, or about 16 percent of the land area of the state, albeit at very low densities. Of all federally listed species in California, the San Joaquin kit fox has by far the greatest overlap with agricultural areas, accounting for about 10 million acres in 14 counties, mostly in the agriculturally rich southern San Joaquin Valley. Other species that are interspersed with agricultural areas include birds, mammals, reptiles, amphibians, crustaceans and many plants.
Science topics	Agriculture, Urban development, Insecticides, Rodenticides, Herbicides, Fungicides, Chinook Salmon, Delta Smelt, Benthos, Shorebirds, Giant garter snake, California tiger salamander, Insects, Other species, Fish, Mammals, Birds, Amphibians and reptiles
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 VemcoÂ® V9 69 kHz acoustic transmitters and released near the point of capture. An array of VemcoÂ® 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 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 â€œDrought Stressor Monitoringâ€. 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	San Francisco Estuary Invasive Spartina Project
Lead	California State Coastal Conservancy
Description	"The Invasive Spartina Project is a coordinated regional effort among local, state and federal organizations dedicated to preserving California's extraordinary coastal biological resources through the elimination of introduced species of Spartina(cordgrass). Introduced cordgrasses are highly aggressive invaders that significantly alter both the physical structure and biological composition of our tidal marshes, mudflats, and creeks. The project also monitors Ridgway Rails (formerly Clapper Rail) and water quality. Funding for the Invasive Spartina Project comes from the CALFED Bay-Delta Program, United States Fish and Wildlife Service Coastal Program, National Fish and Wildlife Foundation, and the California State Coastal Conservancy.
Science topics	Intertidal and transition zones, Saltwater and freshwater marshes, Other species
Updated	April 29, 2022

Title	San Francisco Bay National Estuarine Research Reserve
Lead	National Oceanic and Atmospheric Administration [NOAA]
Description	The National Estuarine Research Reserve System is a network of 29 coastal sites designated to protect and study estuarine systems. Established through the Coastal Zone Management Act, the reserves represent a partnership program between NOAA and the coastal states. NOAA provides funding and national guidance, and each site is managed on a daily basis by a lead state agency or university with input from local partners.
Science topics	Stage, Air temperature, Precipitation, Wind, Solar irradiance, Nitrogen and ammonia, Phosphorous, Chlorophyll A B, Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Intertidal and transition zones, Above highwater refugia, Main channels, Sloughs, Backwater, Mollusks, Saltwater and freshwater marshes, Other species
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	Nutria Eradication Program
Lead	California Department of Fish and Wildlife [CDFW]
Description	CDFW implemented the Nutria Eradication Incident Command System in 2018 to detect, assess, control and eradicate invasive nutria in the Sacramento San Joaquin Delta. The program includes rights of entry, camera traps, trapping and removal of 823 (to date) nutria.
Science topics	Levees, Sloughs, Backwater, Managed ponds, Nutria, Environmental drivers, Socio economic drivers
Updated	April 29, 2022

Title	Perennial Streams Survey
Lead	Southern California Stormwater Monitoring Coalition [SMC]
Description	The Perennial Streams Assessment (PSA) is an ongoing, long-term statewide survey of the ecological condition of wadeable perennial streams and rivers throughout California. The PSA collects samples for biological indicators (BMIs and algae) and chemical constituents (nutrients, major ions, etc.), and also conducts habitat assessments for both in-stream and riparian corridor conditions.
Science topics	Nitrogen and ammonia, Chlorophyll A B, Harmful algal blooms HAB, Main channels, Submerged aquatic vegetation, Benthos, Insects, Mollusks, Crustaceans, Conductivity, Habitat, Invertebrates
Updated	April 29, 2022

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	Aquatic Invasive Species [AIS] Program
Lead	U.S. Fish and Wildlife Service [USFWS]
Description	The overarching AIS goal is that "Risks of aquatic invasive species invasions are substantially reduced, and their economic, ecological, and human health impacts are minimized. This goal is addressed through a series of performance and workload measures. The AIS Program provides funding for Aquatic Invasive Species Coordinators for each Region within the Service and their respective aquatic nuisance species activities. These coordinators work closely with the public and private sector to develop and implement invasive species projects. One of the primary initiatives of the program is the prevention of invasive species via boats through the "100th Meridian Initiative" (overseen by individual AIS regional coordinators). This initiative aims to prevent the spread of aquatic invasive species by boats personal watercraft and other pathways. Through boat inspections and boaters assessments along the 100th meridian, partners can learn how to prevent the spread of zebra mussels and other AIS via transport of boats and personal watercraft.
Science topics	Above highwater refugia, Amphibians and reptiles, Backwater, Brazilian waterweed, Corbicula and Potamocorbula, Crustaceans, Fish, Floating aquatic vegetation, Giant reed, Intertidal and transition zones, Invasive and non native species, Main channels, Mammals, Managed ponds, Mollusks, Mudflats, Nutria, Open water, Riparian wildlife, Saltwater and freshwater marshes, Seasonally flooded, Sloughs, Spongeplant, Striped bass, Submerged aquatic vegetation, Water hyacinth, Yellow star thistle
Updated	June 26, 2025

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	Aquatic Invasive Species Program [CDFW]
Lead	California Department of Fish and Wildlife [CDFW]
Description	The mission of the Invasive Species Program is to reduce the negative effects of non-native invasive species on the wildlands and waterways of California. We are involved in efforts to prevent the introduction of these species into the state, detect and respond to introductions when they occur, and prevent the spread of invasive species that have become established. Our projects address problems with introduced animals and plants, both terrestrial and aquatic. More fundamentally, we try to identify and address the ways by which the species are introduced, typically inadvertently, by human activities. Studies show that preventing introductions is the most effective and cost-efficient way to manage invasive species. We conduct our work in coordination with other government agencies and non-governmental organizations.
Science topics	Habitat, Invasive and non native species, Main channels, Managed ponds, Mollusks, Other species, Recreation and tourism, Saltwater and freshwater marshes, Sloughs, Submerged aquatic vegetation, Vessels and shipping channels
Updated	July 31, 2024

Title	Water Quality in the Nation's Stream and Rivers
Lead	U.S. Geological Survey [USGS]
Description	In 1991, Congress established the National Water-Quality Assessment (NAWQA) Project to address where, when, why, and how the Nation's water quality has changed, or is likely to change in the future, in response to human activities and natural factors. A prominent feature of NAWQA is the development of long-term consistent and comparable information on streams, rivers, ground water, and aquatic systems. The NAWQA Project is designed to answer these questions: 1. What is the current condition of our Nation's streams, rivers, and groundwater? 2. How are these conditions changing over time? 3. How do natural features and human activities affect these conditions, and where are those effects most pronounced? Under the National Water-Quality Assessment (NAWQA) project, there are several surface water and ecology studies, including the Regional Stream Quality Assessment (RQSA) (a baseline assessment of streams), and current conditions and long-term trends monitoring.
Science topics	Wastewater discharge, Nitrogen and ammonia, Phosphorous, Carbon, Chlorophyll A B, Harmful algal blooms HAB, Suspended sediment, Chemistry, Toxicity, Salinity, Water temperature, Dissolved oxygen, pH, Turbidity, Hg and methyl mercury, Polychlorinated biphenyl PCB, Hydrocarbons and polycyclic aromatic hydrocarbons PAH, Flame retardants, Endocrine disruptors, Lead, Cadmium, Copper, Zinc, Arsenic, Selenium, Constituent of emerging concern CEC, Insecticides, Rodenticides, Herbicides, Fungicides, Microplastics, Other discharge contaminants, Main channels, Sloughs, Backwater, Benthos, Insects, Mollusks, Crustaceans, Fish, Invertebrates
Updated	April 29, 2022

Title	National Wetland Condition Assessment [NWCA]
Lead	U.S. Environmental Protection Agency [USEPA]
Description	The National Wetland Condition Assessment (NWCA) is a statistical survey that begins to address some of the gaps in our understanding of wetland health by providing information on the ecological condition of the nation's wetlands and stressors most commonly associated with poor condition. The NWCA is designed to answer basic questions about the extent to which our nation's wetlands support healthy ecological conditions and the prevalence of key stressors at the national and regional scale. It is intended to complement and build upon the achievements of the U.S. Fish and Wildlife Service Wetland Status and Trends Program, which characterizes changes in wetland acreage across the conterminous United States. Paired together, these two efforts provide government agencies, wetland scientists, and the public with comparable, scientifically defensible information documenting the current status and, ultimately, trends in both wetland quantity (i.e., area) and quality (i.e., ecological condition).
Science topics	Above highwater refugia, Benthos, Chemistry, Chlorophyll A B, Conductivity, Crustaceans, Dissolved oxygen, Drought, Fecal coliform E coli, Fish, Fishing, Floating aquatic vegetation, Flood, Forests, Groundwater, Habitat, Harmful algal blooms HAB, Hg and methyl mercury, Insects, Intertidal and transition zones, Invertebrates, Managed ponds, Mollusks, Mudflats, Nature-based solutions, Nitrogen and ammonia, Open water, Other discharge contaminants, Other species, Other zooplankton, Pelagic fish, pH, Phosphorous, Phytoplankton, Riparian wildlife, Salinity, Saltwater and freshwater marshes, Seasonally flooded, Submerged aquatic vegetation, Surface water flow, Suspended sediment, Tides, Toxicity, Turbidity, Wetlands
Updated	January 29, 2026

Title	Sacramento Watershed Coordinated Monitoring Program [SWCMP]
Lead	Central Valley Regional Water Quality Control Board [Central Valley RWQCB]
Description	SWCMP is a coordinated monitoring effort between DWR and Central Valley RWQCB. This program monitors ambient water quality at locations in the Sacramento River starting upstream of Lake Shasta and going south to Verona, and at the lower end of all large streams tributary to the Sacramento River. It is funded jointly by DWR Northern District Water Quality Section and the Central Valley RWQCB SWAMP. The SWCMP is designed to meet the monitoring needs of the Regional Boardâ€™s Surface Water Ambient Monitoring Program (SWAMP) and the DWR Northern Districtâ€™s Water Quality and Biology section. Coordination allows both agencies to maximize the use of their limited resources.
Science topics	Nitrogen and ammonia, Phosphorous, Carbon, Suspended sediment, Toxicity, Water temperature, Dissolved oxygen, pH, Turbidity, Lead, Cadmium, Copper, Zinc, Arsenic, Selenium, Other discharge contaminants, Main channels, Sloughs, Backwater, Benthos, Insects, Mollusks, Crustaceans, Conductivity, Invertebrates
Updated	April 29, 2022

Title	Bioassessment Program
Lead	California Department of Fish and Wildlife [CDFW]
Description	Biological assessment (bioassessment) is an evaluation of the condition of a waterbody based on the organisms living within it. It involves surveying the types and numbers of organisms present in the water and comparing the results to established benchmarks of biological health. Scientists and managers around the world use this approach to directly and quantitatively measure the ecological health of a waterbody and to monitor the cumulative impacts of environmental stressors on surface waters. Benthic macroinvertebrates (BMIs) and benthic algae are the primary biota used for bioassessments in California. BMIs are a diverse group of small but visible animals that live at the bottom of rivers and streams. They are comprised mostly of aquatic insects but also include crustaceans, mollusks, and worms. BMI assemblages are found in most waterbodies and are reliable indicators of biological health because they are relatively stationary and respond predictably to a variety of environmental stressors. Benthic algae are also sensitive to environmental stressors and provide environmental condition information that is often complementary to that derived from BMI assemblages. Because of their short lifespans and rapid reproduction rate, algae can respond quickly to changing water conditions. They are also more directly responsive to nutrients (such as nitrogen and phosphorus) and are therefore suited for monitoring nutrient runoff, one of the major environmental stressors in California. SWAMP began conducting bioassessment in 2000. The program continues to work closely with the California Department of Fish and Wildlife's (CDFW) Aquatic Bioassessment Laboratory, which has been the primary producer of this technical work.
Science topics	Salinity, Water temperature, Main channels, Insects, Mollusks, Crustaceans, Conductivity, Other species, Invertebrates
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	Central Valley Chinook Adult Escapement Monitoring Project
Lead	California Department of Fish and Wildlife [CDFW]
Description	The Central Valley Chinook Salmon In-river Escapement Monitoring Plan is a science-based collaborative approach to improve monitoring of adult Chinook salmon returning from the ocean to spawn in CV streams (escapement) and harvested in freshwater. Accurate estimates of escapement are critical to sound management of ocean and inland harvest and monitoring the recovery of listed stocks. A result of requests from fisheries resource managers, the development of this plan was funded in 2007 by the CALFED Ecosystem Restoration Program. The comprehensive monitoring plan includes a spatially and temporally balanced sampling protocol that when implemented will allow for statistically defensible estimates of population status. The plan incorporates an adaptive management strategy, and recommends a standardized database structure, as well as standardized reporting techniques.
Science topics	Main channels, Chinook Salmon
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	Fisheries Branch Anadromous Assessment
Lead	California Department of Water Resource [DWR]
Description	The Fisheries Branch Anadromous Assessment Unit compiles annual population estimates of Chinook salmon, Oncorhynchus tshawytscha. Estimates are based on counts of fish entering hatcheries and migrating past dams, carcass surveys, live fish counts, creel census data, and ground and aerial redd counts.
Science topics	Main channels, Sloughs, Backwater, Seasonally flooded, Open water, Chinook Salmon
Updated	April 29, 2022

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	Freshwater CyanoHABs Program [Blue-Green Algae Harmful Algal Blooms]
Lead	California State Water Resources Control Board [SWRCB]
Description	Observations of harmful algal blooms (HABs) and algal toxins have increased globally in recent years. HABs are problematic because they can affect multiple beneficial uses including recreation, aquatic life, and drinking water by reducing aesthetics, lowering dissolved oxygen concentration, causing taste and odor problems, and producing potent toxins. Water Board staff are working with state and local entities to identify and respond to HAB incidents throughout California. The Water Board first began to formally address this issue in 2005 when it formed the Blue Green Algae Work Group, later renamed the California Cyanobacteria Harmful Algal Bloom Network (CCHAB). An initial product of this group was the Voluntary Guidance Document (original release 2010, updated 2016). Subsequently, SWAMP prepared California Freshwater HAB Assessment and Support Strategy to articulate a coordinated program to assess, communicate and manage HABs in California.
Science topics	Main channels, Sloughs, Backwater, Submerged aquatic vegetation, Floating aquatic vegetation, Benthos, Saltwater and freshwater marshes, Environmental drivers, Socio economic drivers, Other species
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	Striped Bass Study
Lead	California Department of Fish and Wildlife [CDFW]
Description	Staff of the Striped Bass Study calculate adult Striped Bass 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 adult Striped Bass 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 adult Striped Bass and monitoring the subsequent ratio of tagged fish to untagged fish, we calculate adult Striped Bass abundance, relative abundance, harvest rate, and survival rate. During April and May we use large traps near Knights Landing and nets near Antioch to collect adult Striped Bass, 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	Water temperature, Main channels, Striped bass
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	EMP Zooplankton Study
Lead	California Department of Fish and Wildlife [CDFW]
Description	The Environmental Monitoring Program (EMP) has conducted the Zooplankton Study since 1972 to better assess trends in the lower trophic food web in the San Francisco Bay-Delta estuary. The study also detects and monitors zooplankton recently introduced to the estuary and determines their effects on native species. Under the auspices of the Interagency Ecological Program for the San Francisco Estuary and mandated by Water Right Decision D-1641, the EMP Zooplankton Study is part of the Environmental Monitoring Program and is conducted by the California Department of Fish and Game (CDFW), California Department of Water Resources (DWR), and the United States Bureau of Reclamation (USBR).
Science topics	Crustaceans, Invertebrates, Main channels, Mysis, Other zooplankton, Sloughs
Updated	October 16, 2024

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	Breeding Waterfowl Surveys
Lead	Pacific Flyway Council
Description	The California breeding population survey is modeled after the continental breeding survey. Though most of the wintering waterfowl in California breed outside of the state, California still has a significant number that both breed and winter here. CDFW and California Waterfowl Association (CWA) biologists conduct the California survey. Surveyed areas include wetland and agricultural areas in northeastern California, throughout the Central Valley, the Suisun Marsh, and some coastal valleys. CDFW biologists and warden-pilots use a fixed-wing aircraft to fly all of the transects while CWA completes the "ground" portion of the survey using a helicopter. This survey also utilizes a visibility correction factor. For the most part, ducks that only winter in California comprise most of the harvest, but CDFW augments the continental survey assessment with the estimates of California's breeding population for developing hunting regulation recommendations.
Science topics	Mudflats, Intertidal and transition zones, Above highwater refugia, Main channels, Sloughs, Backwater, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Delta islands, Pacific flyway, Waterfowl, Saltwater and freshwater marshes, Non resident and overwintering birds
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	Hunting Licenses [waterfowl]
Lead	California Department of Fish and Wildlife [CDFW]
Description	California monitors the number of hunting licenses, including waterfowl, issued by year, county and type throughout the state. They also produce annual hunting results documents that show the number of hunters, the number of animals caught, and other information pertaining to the animals, broken down by county.
Science topics	Hunting, Waterfowl, Environmental drivers
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	Delta Region Areawide Aquatic Weed Project [DRAAWP]
Lead	California Department of Parks and Recreation [PARKS]
Description	The Delta Region Areawide Aquatic Weed Program has been focusing science and the application of science onto the management of invasive aquatic weeds such as water hyacinth, Brazilian egeria, and water primrose in the Delta.
Science topics	Above highwater refugia, Backwater, Delta islands, Floating aquatic vegetation, Giant reed, Habitat, Intertidal and transition zones, Main channels, Sloughs, Submerged aquatic vegetation
Updated	November 29, 2022

Title	Invasive Species Program
Lead	California Department of Fish and Wildlife [CDFW]
Description	The mission of the Invasive Species Program is to reduce the negative effects of non-native invasive species on the wildlands and waterways of California. We are involved in efforts to prevent the introduction of these species into the state, detect and respond to introductions when they occur, and prevent the spread of invasive species that have become established. The Quagga/Zebra program particularly relies heavily on water quality data, as the species will not establish in waters with low calcium. Therefore they rely substantially on water quality data collected and housed by others (primarily DWR). A large part of their effort is in training other state or private recreational agencies to recognize and report the species, and therefore also reported by others.
Science topics	Mudflats, Intertidal and transition zones, Main channels, Sloughs, Backwater, Submerged aquatic vegetation, Floating aquatic vegetation, Open water, Managed ponds, Waterfowl, Insects, Mollusks, Crustaceans, Corbicula and Potamocorbula, Nutria, Water hyacinth, Brazilian waterweed, Spongeplant, Giant reed, Yellow star thistle, Saltwater and freshwater marshes, Other species, Mammals, Amphibians and reptiles, Invasive and non native species
Updated	April 29, 2022

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	Atmospheric River Reconnaissance
Lead	University of California - San Diego [UCSD]
Description	CW3E works directly with water managers in the West to develop science and tools designed to better prepare for the variability inherent in the western US climate. Atmospheric River (AR) Reconnaissance (AR Recon) campaigns support improved prediction of landfalling ARs on the U.S. west coast. ARs are a type of storm that is key to the region's precipitation, flooding, and water supply. Forecasts of landfalling ARs are critical to precipitation prediction and yet are in error by +/- 400 km at even just 3-day lead time (see figure to the right;Wick et al. 2013). The concept for AR Recon was first recommended in a report to the Western States Water Council (Ralph et al. 2014) that was prepared by a broad cross-disciplinary group in 2013. AR Recon was conducted with 3 missions in 2016, 6 in 2018, and 6 in 2019. USACE and the California Department of Water Resources were key sponsors of the AR Recon 2018 and 2019 campaigns. Aircraft that are normally used for hurricane reconnaissance were deployed over the northeast Pacific to collect observations to support improved AR forecasts. The data were assimilated by global modeling centers in real-time.
Science topics	Flood, Air temperature, Precipitation, Wind, Extreme storms, Chinook Salmon, Snowpack and snow water equivalent SWE
Updated	April 29, 2022

Title	Mid-Winter Waterfowl Survey [MWS]
Lead	U.S. Fish and Wildlife Service [USFWS]
Description	Some geese and ducks are not adequately monitored during the spring and summer because they nest in areas not well covered by breeding population surveys. Abundance indices for these species are obtained from surveys on wintering areas. Most of these surveys are targeted at specific species or populations. A nationwide effort to survey all waterfowl is conducted annually in January. This, the Mid-winter Waterfowl Survey, provides information on population trends for some species, distribution on the wintering grounds, and habitat use. The Mid-Winter Waterfowl Survey is conducted cooperatively by the states and the U.S. Fish and Wildlife Service.
Science topics	Hunting, Waterfowl
Updated	April 29, 2022

Title	Central Valley Joint Venture [CVJV]
Lead	U.S. Fish and Wildlife Service [USFWS]
Description	The Central Valley Joint Venture (CVJV) is a self-directed coalition consisting of 21 State and Federal agencies, private conservation organizations and one corporation. This partnership directs their efforts toward the common goal of providing for the habitat needs of migrating and resident birds in the Central Valley of California. The CVJV was established in 1988 as a regional partnership focused on the conservation of waterfowl and wetlands under the North American Waterfowl Management Plan. It has since broadened its focus to the conservation of habitats for other birds, consistent with major national and international bird conservation plans and the North American Bird Conservation Initiative. The Central Valley Habitat Joint Venture was formally organized in 1988 and was one of the original six priority joint ventures formed under the NAWMP. Renamed the Central Valley Joint Venture in 2004, the Management Board now consists of nineteen public and private members. The CVJV is currently administered through a coordination office within the U.S. Fish and Wildlife Service, and is guided by a Management Board that receives input and recommendations from a variety of working committees.
Science topics	Hunting, Agriculture, Urban development, Recreation and tourism, Mudflats, Intertidal and transition zones, Above highwater refugia, Seasonally flooded, Riparian wildlife, Waterfowl, Shorebirds, Gulls, Habitat, Non resident and overwintering birds
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	From Microbes to Zooplankton, What Defines a Beneficial Wetland?
Lead	San Francisco State University, Estuary & Ocean Science Center
Description	Our study will characterize species diversity at multiple levels of biological organization in the water column of restoring wetlands in the upper San Francisco Estuary and Delta (SFE), from bacteria to fishes. In doing so, we will also describe the foodweb benefits being provided to larval fishes, including longfin smelt, through additional dietary DNA analysis. We will use the species diversity we find in the water column to identify a subset of biota that are indicative of the conditions present in wetlands in different stages of restoration (early, intermediate, and mature) and identify connections between those indicators to the foodweb resources being provided to higher trophic levels. We will study 3-4 wetlands in each of 3 stages: early (unvegetated), intermediate (partially vegetated and partially channelized), and mature (fully vegetated and channelized) wetlands.
Science topics	Crustaceans, Cyanobacteria, Estuaries, Fish, Food webs, Habitat, Habitat restoration, Insects, Invertebrates, Longfin Smelt, Other species, Other zooplankton, Pelagic fish, Phytoplankton, Predation, Restoration, Salinity, Saltwater and freshwater marshes, Tidal wetlands, Wetlands, Zooplankton
Updated	January 31, 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	Impacts of predation and habitat on Central Valley Chinook smolt survival
Lead	University of Vermont, USGS Vermont Cooperative Fish and Wildlife Research Unit
Description	The Sacramento River in California’s Central Valley has been highly modified over the past 150 years due to mining, urbanization, and impoundment/diversion of river flow to provide water for municipal, industrial, and agricultural needs. Land use changes combined with high levels of harvest have been accompanied by drastic declines in native salmon populations, including the once abundant Chinook salmon (Oncorhynchus tshawytscha). Further, the region has been subject to the introduction and widespread establishment of non-native fish species, some of which are predators of juvenile salmon. Of the four historic ecotypes of Chinook salmon (fall, late-fall, winter, and spring runs), winter- and spring-runs have been most impacted and are currently listed as endangered and threatened respectively under the US Endangered Species act. Past research has illustrated how smoltification of juvenile salmon and outmigration from freshwater to the ocean is a time of increased mortality, and reduced survival at this life stage can impact the number of reproducing adults returning to the system in subsequent years. While these studies have provided valuable information on how habitat and environmental conditions experienced by migrating Chinook salmon smolts can affect survival, they have primarily focused on individual ecotypes during the portion of the year where downstream migrations occur. However, variation in smolt size and migration timing among ecotypes can expose migrating fish to differing environmental conditions and levels of exposure to predation, which can present distinct risks for outmigration survival. To identify the areas and environmental conditions which have the greatest relative impact on juvenile survival for each ecotype, this project will use over ten years of data (2012-2022) from acoustically tagged smolts representing all four Chinook salmon ecotypes in the Sacramento River/Central Valley. Combining these data will increase sample size relative to previous studies, the range of environmental conditions (e.g., temperature, flow, and predator abundance) modeled, the range of fish sizes, and thus, the statistical power of our analyses. We hypothesize that each ecotype will have different factors that will be the primary drivers of mortality experienced during outmigration. To test our hypotheses, we will implement Cormack-Jolly-Seber (CJS) mark-recapture models to estimate both the probability of survival through reaches of the Sacramento River delineated by acoustic receivers, and the detection probability in each reach. Survival will be modeled as a function of individual, release group, reach-specific, and time-varying covariates. Further, to examine the relative impact of predation on smolt survival, we will include an additional covariate representing predator-prey encounter rates using the Mean Free-path Length model. Finally, model selection will be applied to a series of CJS models to assess the relative impact of each covariate on smolt survival for each of the four Chinook ecotypes.
Science topics	Chinook Salmon, Environmental drivers, Fish, Flows, Habitat, Predation, Salmon migration, Water temperature
Updated	February 2, 2024

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	Delta Invasive Species Symposium
Lead	Delta Interagency Invasive Species Coordination Team [DIISCT]
Description	Since 2015, the DIISC Team has organized a biennial Delta Invasive Species Symposium. The symposium is a forum for Delta managers, researchers, and decision-makers to meet, share and synthesize information, and communicate best practices and lessons learned. https://deltaconservancy.ca.gov/diisc-team-activities/
Science topics	None specified
Updated	April 16, 2026

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