Science activities

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.

The California Recreational Fisheries Survey (CRFS) mission is to collect fishery-dependent data on California's marine recreational fisheries, and to accurately estimate catch and effort in a time frame and on a scale that meets management needs. CRFS collects the data necessary to estimate catch and effort for California's diverse recreational finfish fisheries which range from the California-Mexico border to the California-Oregon border extending over 1,100 miles of coast and is surveyed at over 400 sampling sites. Annually, CRFS conducts over 7,000 sampling assignments and contacts over 68,000 fishing parties. High sampling rates produce confidence in estimates with a 20 percent sample rate of private boat anglers during salmon or groundfish seasons. CRFS collects the data to produce the estimates for all sport-caught finfish.

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.

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

The Environmental Monitoring Program (EMP) began in 1975 to conduct baseline and compliance monitoring of water quality, phytoplankton, zooplankton, and benthic invertebrates in the San Francisco Bay-Delta estuary. This monitoring program was designed to track the impact of water diversions to the State Water Project (SWP) and Central Valley Project (CVP) on the Bay-Delta. In the decades since, EMP scientists have monitored these constituents at fixed and floating stations throughout the estuary and ensured compliance with state and federal mandates such as Water Right Decision 1641 (D-1641). In the years and decades since its inception, EMP has become one of the cornerstones for scientists' and managers' understanding of the pace and pattern of change in this critical ecosystem. By sampling water quality and biological communities concurrently, EMP has created a dataset that is uniquely useful in better understanding causal connections between physical, biological, and biogeochemical processes. 

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.

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).

Managing California’s water supply is complex, requiring careful coordination to ensure sustainability, water quality, and the protection of public and environmental health. In the Sacramento–San Joaquin Bay-Delta, hundreds of datasets from studies and monitoring programs are used to assess conditions and inform key operational decisions. However, these datasets are often fragmented across agencies and stored in inconsistent formats, making it time-consuming for analysts and researchers to locate and use the data effectively.

This project aims to enhance the Bay-Delta Live (BDL) data management platform (www.baydeltalive.com) by integrating datasets from the California Department of Water Resources’ Water Data Library (WDL). The primary focus is on water quality and environmental monitoring data. By streamlining access to these resources, the project will improve the discovery, retrieval, and analysis of water-related datasets across multiple sources.

Key outcomes include:

• Unified access to quality-controlled, time-series water data;
• Enhanced spatial visualization and modeling capabilities;
• Improved collaboration among agencies and stakeholders through shared tools and insights.

This work will support more informed decision-making and help ensure the long-term safety, reliability, and ecological integrity of California’s water resources.

High-frequency monitoring for hydrodynamic (stage, velocity, flow), water quality (including chlorophyll, nutrients), sediment, and phytoplankton at key locations in the Delta (Figure 1). The physical properties monitored by the fixed-station network are the primary drivers of the habitat conditions and biological responses that management actions are designed for. Combined, these data establish the spatially and temporally rich data set needed for real-time operation of water export facilities, understanding Delta ecosystem responses to hydrological conditions, and evaluating restoration actions.

For more information, including data links, please see the USBR program webpage.