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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	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/Potamocorbula, Water hyacinth, Brazilian waterweed, Spongeplant, Giant reed, Yellow star thistle, Invasive / non native species
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 / 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/Potamocorbula, Nutria, Water hyacinth, Brazilian waterweed, Spongeplant, Giant reed, Yellow star thistle, Saltwater / freshwater marshes, Habitat, Other species, Fish, Mammals, Birds, Amphibians and reptiles, Invertebrates, Invasive / non native species, Non-resident / overwintering birds
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.â€ 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	Mudflats, Intertidal / transition zones, Above-highwater refugia, Main channels, Sloughs, Backwater, Submerged aquatic vegetation, Floating aquatic vegetation, Seasonally flooded, Open water, Managed ponds, Riparian wildlife, Mollusks, Crustaceans, Striped bass, Corbicula/Potamocorbula, Nutria, Water hyacinth, Brazilian waterweed, Spongeplant, Giant reed, Yellow star thistle, Saltwater / freshwater marshes, Fish, Mammals, Amphibians and reptiles, Invasive / non native species
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, fish screens & passage
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	Summer Townet Survey
Lead	California Department of Fish and Wildlife [CDFW]
Description	The Summer Townet (STN) Survey was initiated in 1959 to determine relative distribution and abundance of young of the year (age-0) striped bass (Morone saxatilis) in the Delta. To predict fishery recruitment, the survey calculates an index to measure age-0 striped bass year class strength. This index is based on abundance when age-0 striped bass attain a mean length of 38.1 mm. In contrast, the delta smelt (Hypomesus transpacificus) index is the average of the first two survey indices. The delta smelt index was developed about 1990 in response to declining delta smelt abundance. It has proven valuable in gauging the health of the estuary;delta smelt abundance trend data was used as supporting evidence for their listing as threatened in 1992 under the Federal and State Endangered Species Acts. It appears that zooplankton data are also collected.
Science topics	Mysis, Other zooplankton, Main channels, Sloughs, Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Striped bass, Fish
Updated	April 29, 2022

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/Potamocorbula, Conductivity, Environmental drivers, Other species, Fish, Invertebrates
Updated	April 29, 2022

Title	Fish Salvage and Genetic Analysis
Lead	U.S. Bureau of Reclamation [USBR]
Description	The State Water Project (SWP), operated by the California Department of Water Resources (DWR), and the Central Valley Project (CVP), operated by the U.S. Bureau of Reclamation, export water out of the San Francisco Bay Delta for urban and agricultural use in California. Salvage of fish at both facilities is conducted 24 hours a day, seven days a week at regular intervals. Since 1957, the U.S. Bureau of Reclamation (USBR) has salvaged fish at the Tracy Fish Collection Facility (TFCF). CDFW's Fish Facilities Unit, in cooperation with DWR, began salvaging fish at the Skinner Delta Fish Protective Facility (SDFPF) in 1968. Fish salvage and loss rates are used to determine the need for changes in operations in response to National Marine Fisheries Service (NMFS) regulatory requirements. Salvage and loss monitoring includes daily monitoring and reporting of estimated loss of salvaged fish, as well as monitoring and reporting of salvaged Coded Wired Tagged (CWT) hatchery fish. This information is widely used by West Coast fisheries agencies to collect information on natural and hatchery-reared stocks of salmon and steelhead. Our state-of-the-art genetic analysis techniques are used to quantify salvage rates of listed runs of California's Central Valley juvenile Chinook Salmon. We also utilize advanced genetic analysis techniques to identify different populations of Central Valley juvenile Chinook Salmon, and actively participate in development of new analysis methods.
Science topics	Chinook Salmon, Steelhead Trout, Green sturgeon, White Sturgeon, Delta Smelt, Longfin Smelt, Sacramento Splittail, Striped bass, Fish, Invasive / non native species
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 / transition zones, Invasive / non native species, Invertebrates, Longfin Smelt, Main channels, Nitrogen, Nitrogen / ammonia, Nutrients, Other species, Other zooplankton, Pelagic fish, pH, Phytoplankton, Primary production, Sacramento Splittail, Salmon migration, Salmon rearing, Saltwater / freshwater marshes, SAV/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	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 / non native species, Invertebrates, Longfin Smelt, Mollusks, Pelagic fish, Restoration, Restoration planning, Sacramento Splittail, Salmon migration, Salmon rearing, Steelhead Trout, Striped bass, Sturgeon, Tidal wetlands, Wetlands, White Sturgeon
Updated	May 24, 2024

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

Title	Standard Operating Procedure for Diagnosing and Addressing Predator Detections in Salmon Telemetry Data
Lead	University of Washington [UW]
Description	Tag predation is a complicating factor in juvenile salmon telemetry studies that can bias results, delay timely reporting, and prevent effective data synthesis. This project addresses the problem by (1) characterizing predatory fish movement patterns from existing telemetry data in the Delta; (2) developing a standard operating procedure for diagnosing and handling detections of predated tags in salmon telemetry studies; and (3) implementing the recommendations in a software package in Program R that includes code, a “library” of expected predator behaviors, and example vignettes. The R package will be freely available for download at www.cbr.washington.edu.
Science topics	Chinook Salmon, Endangered species, Fish, Intertidal / transition zones, Invasive / non native species, Predation, Salmon migration, Steelhead Trout, Striped bass
Updated	December 26, 2023

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