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 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.
Under the 2008, 2019, 2024 State Water Project/Central Valley Project Joint Operations Biological Opinion from United States Fish and Wildlife Service, 2009, 2019, 2024 National Marine Fisheries Service, and 2009, 2020, and 2024 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.
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 including use by rearing salmonids and characterization of the predator and competitor communities
The Zooplankton Study has sampled macro-, meso-, and micro-zooplankton in the upper San Francisco Estuary since 1972. Samples are collected monthly at 19 stations, located from upper San Pablo Bay to the eastern Delta, using three gear types – a pump sampler for microzooplankton, such as copepod nauplii and rotifers, a CB net for mesozooplankton, such as adult copepods and cladocerans, and a mysid net for macrozooplankton. The Zooplankton Study provides data on zooplankton abundance and distribution to assess the food resources available to fish in the upper San Francisco Estuary, as zooplankton are an important trophic link between primary producers and upper trophic levels. This information is used by aquatic ecologists to investigate physical and biological drivers of the lower food web and relationships between food resources and fishes that feed on zooplankton in the upper estuary, including listed species such as Delta and Longfin Smelt.
The Zooplankton Study is conducted in compliance with the SWRCB’s Water Rights Decisions 1485 (Term 10a) and 1641 (Term 11a). This study may also inform the CDFW 2024 Incidental Take Permit, the operations of the State Water Project (Table 2), the 2024 NMFS and USFWS Biological Opinions for operations of the Central Valley Project, and the Summer-Fall Habitat Action Team.
