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11 results for “Interagency Ecological Program for the San Francisco Estuary”
Interagency Ecological Program: Integrated Dataset of Phytoplankton Enumeration Data in the San Francisco Estuary, 1992-2024
Phytoplankton community composition is an important driver of zooplankton productivity and food supply for higher trophic levels in the San Francisco Estuary. Various monitoring surveys throughout the region collect phytoplankton enumeration data dating back to the 1990s. These include surveys from the CA Department of Water Resources (CADWR), CA Department of Fish and Wildlife (CDFW), the US Bureau of Reclamation (USBR), and the US Geological Survey (USGS). These surveys collect data via various sampling and laboratory methods which are not always directly comparable. This integrated dataset includes both enumeration counts and well-documented metadata to allow for informed decision-making in the integration of these data. It also standardizes taxonomic names between groups via a key list. Note that, in this dataset, we make conservative decisions about taxonomic resolution to ensure maximum compatibility between groups. For more detailed metadata and higher taxonomic resolution, refer to individual surveys’ publications or reach out to their primary contact.
Interagency Ecological Program and US Fish and Wildlife Service: San Francisco Estuary Enhanced Delta Smelt Monitoring Program Data, 2016-2024
The Enhanced Delta Smelt Monitoring Program (EDSM) was initiated by the U.S. Fish and Wildlife Service in 2016. The main purpose of EDSM is to provide information about endemic Delta Smelt (Hypomesus transpacificus) population sizes and distributions within the upper San Francisco Estuary. To track the life cycle of this annual species, larval trawling with a fine-mesh (20 mm) net is conducted during the spring months, and Kodiak trawling for juveniles and adults occurs during the summer, fall, and winter months. Sampling sites are chosen via a stratified random sampling design. A minimum of two tows are conducted at each site, and field staff typically sample between 18 and 41 sites weekly. All fish collected are identified and enumerated, and a subset are measured for body length. Environmental data (water temperature, conductivity, dissolved oxygen, turbidity, depth) are also measured. In addition to Hypomesus spp., this long-term monitoring dataset can also be useful in evaluating the status and trends of other species of interest, especially pelagic fishes. For more information: https://www.fws.gov/office/lodi-fish-and-wildlife
Interagency Ecological Program: Zooplankton abundance in the Upper San Francisco Estuary from 1972-2021, an integration of 7 long-term monitoring programs
The upper San Francisco Estuary is an inland inverse delta formed by the confluence of 5 major rivers that drain 40% of the land in California (USA). It is a central hub of water delivery in California and home to a number of commercially important and endangered fish, such as Chinook Salmon, Green Sturgeon, and Delta Smelt. To monitor the environmental impacts of water exports from this system, extensive ecological monitoring has been conducted since the 1960s. To track lower trophic levels, zooplankton abundance has been monitored from 1972 to present. Starting with just one survey (the CA Department of Water Resources’ [CDWR] and California Department of Fish and Wildlife’s [CDFW] Environmental Monitoring Program) in 1972, the suite of zooplankton surveys gradually expanded with time. Several surveys traditionally focused on monitoring fish abundance added zooplankton nets to their sampling programs. The CDFW 20-mm larval fish survey added zooplankton sampling in 1995, the CDWR Yolo Bypass Fish Monitoring Program add zooplankton in 1999, the CDFW Summer Townet Survey added zooplankton in 2005, and the Fall Midwater Trawl added zooplankton in 2007. Two new sampling programs, the Fish Restoration Program and Directed Outflow Project, began in 2015 and 2017, respectively. All sampling programs continue today. Each survey samples once or twice monthly at set of fixed or random stations that varies across surveys depending on their objectives. While the Environmental Monitoring Program samples year-round, the other surveys are mostly seasonal, although additional months were sampled in some years. Most surveys target open channels although the Fish Restoration Program samples in or near shallow tidal wetlands. Three size classes of zooplankton are targeted by these sampling programs with different net mesh sizes: micro zooplankton (copepods and rotifers) are targeted with a 43 µm mesh net, meso zooplankton (copepods and cladocerans) are targeted with 150 - 160 µm mesh
Interagency Ecological Program: Over four decades of juvenile fish monitoring data from the San Francisco Estuary, collected by the Delta Juvenile Fish Monitoring Program, 1976-2025
The United States Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP) has monitored juvenile Chinook Salmon Oncorhynchus tshawytscha and other fish species within the San Francisco Estuary (Estuary) since 1976 using a combination of surface trawls and beach seines. Since 2000, three trawl sites and 58 beach seine sites have been sampled weekly or biweekly within the Estuary and lower Sacramento and San Joaquin Rivers. As part of the Interagency Ecological Program (IEP) that manages the Estuary, the DJFMP has tracked the relative abundance and distribution of naturally and hatchery produced juvenile Chinook Salmon of all races as they outmigrate through the Sacramento-San Joaquin Delta for over four decades. The data that DJFMP collected has been used not only to help inform the management of Chinook Salmon, but also to monitor the status of native species of interest such as the previously listed Sacramento Splittail Pogonichthys macrolepidotus and invasive species such as Mississippi Silverside Menidia audens and Largemouth Bass Micropterus salmoides. DATA CORRECTION/UPDATE: Previous data versions 244.6, 244.7, and 244.8 contained an error and resulted in duplicated records of hatchery Chinook Salmon in the datasets. These datasets were removed from the data repository and the error was corrected in version 244.9 and after. DNA Data: Full more details of the DNA methods and results for juvenile Chinook salmon included in this dataset, please check out Blankenship, S.M., J. Israel, E. Buttermore, and K. Reece. 2021. Knights Landing, California Department of Fish and Wildlife, Genetic Determination of Population of Origin 2017 through 2019 ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/85fbc988c0b1362e84c318e69c7a939e. For more information on the Delta Juvenile Fish Monitoring Program: https://www.fws.gov/project/delta-juvenile-fish-monitoring-program
Interagency Ecological Program San Francisco Estuary Smelt Larva Survey 2009 – 2025
The Interagency Ecological Program's Smelt Larva Survey was initiated by the California Department of Fish and Wildlife (CDFW) in 2009 to monitor the distribution and abundance of newly hatched Longfin Smelt (Spirinchus thaleichthys) in the San Francisco Estuary. Surveys are conducted bi-weekly, and sampling begins in December and continues through mid-March. The SLS samples at fixed stations, from San Pablo Bay through Suisun Bay and into the Sacramento-San Joaquin River Delta. Napa River stations were added in 2014 and the San Pablo Bay expansion stations were added in December 2022. Each sampling week currently consists of 59 stations. At each station, one 10-minute stepped oblique (bottom to top) tow is conducted following a prescribed tow schedule. The net is a conical 500 µm mesh lashed to a D-shaped frame mounted on skis. Larval fish samples are preserved in the field in 10% formalin and brought back to the CDFW Stockton Lab for identification and enumeration under a microscope. Several types of data are collected at each station in addition to the larval fish sample, including the volume of water sampled by the net, surface water temperature, surface and bottom specific conductance (EC normalized at 25˚C), Secchi disk depth, tow duration, tidal condition, and surface water turbidity.
Interagency Ecological Program: Zooplankton and water quality data in the San Francisco Estuary collected by the Summer Townet and Fall Midwater Trawl monitoring programs.
The Interagency Ecological Program’s (IEP) Summer Townet Survey (STN) and Fall Midwater Trawl (FMWT) are two long-term monitoring projects conducted by the California Department of Fish and Wildlife (CDFW) to monitor fish abundance and distribution trends in the San Francisco Estuary (SFE) since 1959 and 1967, respectively. Starting in 2005, zooplankton monitoring was added and paired with fish tows to investigate food availability for young fishes. Food limitation has been a long-term issue and a focus of the Pelagic Organism Decline (POD) studies that began in 2005. By 2011, STN routinely conducted zooplankton monitoring at 40 stations, and FMWT at 32 stations in the upper SFE from Carquinez Strait to the Sacramento Deep Water Ship Channel and into the South Delta. STN samples every other week from June to August and FMWT samples once monthly from September to December. Both projects collect mesozooplankton samples using a modified Clarke-Bumpus (CB) net to target copepods and cladocerans, and FMWT also samples macrozooplankton (i.e. mysids and amphipods) using a mysid net. Flowmeters are used to measure the volume sampled to determine zooplankton catch per unit effort. Environmental variables such as water temperature, turbidity, secchi, and electrical conductivity are collected with each zooplankton sample. Concurrent fish and zooplankton tows conducted by STN and FMWT have allowed for comparisons of fish diet to the available zooplankton prey at the time of collection.
Interagency Ecological Program: Summer Townet Survey for Young Pelagic Fishes in the San Francisco Estuary
The Interagency Ecological Program’s (IEP) Summer Townet Survey (STN) is a long-term effort to monitor the annual recruitment success of young pelagic fishes in the upper San Francisco Estuary (California, United States). Conducted by the California Department of Fish and Wildlife (CDFW) since 1959, STN has sampled fixed 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 Channel (SDWSC) and Cache Slough (CS). Currently, 40 stations are sampled as a “survey” every other week June through August for 6 surveys. A conical net, lashed to a fixed metal “D” frame, is pulled obliquely through the water column 2 to 3 times at each station. All fish and macro-invertebrates are identified and enumerated from each tow, with fork lengths (mm) of the first 50 of each fish species also recorded. Fish catch, length-frequency, and catch-per-unit-effort (CPUE) among stations is available with data visualization tools on the study website for all species (https://wildlife.ca.gov/Conservation/Delta/Townet-Survey). Data collected at historic 31 stations are used to calculate annual relative abundance indices for age-0 Striped Bass (Morone saxatilis) and Delta Smelt (Hypomesus transpacificus). The remaining 9 stations are sampled to expand our sampling range further upriver and increase our understanding of larval and juvenile fish abundance and distribution in the lower Napa River and the North Delta. A meso-zooplankton net targeting copepods and cladocerans is also used in parallel to assess fish food resources at each station and a subset of the fish collected are retained for diet analysis by CDFW researchers (beginning 2005, see STN and FMWT zooplankton data on EDI). The STN also measures habitat conditions via water temperature (°C), water clarity (Secchi disk depth in cm), Turbidity (NTU) and s
Interagency Ecological Program: Data for Synthesis for Ecological Impacts of Drought in the Upper San Francisco Estuary, 1975-2021
These data were collected for the special issue on Drought in the Sacramento-San Joaquin Delta published in San Francisco Estuary and Watershed Sciences, Volume 22, Issue 1, March of 2024. Multi-year droughts are important and impactful features of California’s Mediterranean climate and can fundamentally affect the water quality and the ecosystem response of the San Francisco Estuary and the Sacramento-San Joaquin Delta. This data set was assembled from data collected by long-term monitoring programs over the past 46 years (1975-2021) to evaluate how the estuary changed during multi-year droughts. Data include fish, zooplankton, jellyfish, clams, temperature, Secchi depth, and salinity as measured by fish and water quality surveys, as well as nutrients and chlorophyll measured by water quality surveys. These data are accompanied by hydrologic metrics including Delta Inflow, Delta Outflow, the position of the 2-PSU isohaline, residence time, and daily values of various continuous water quality stations located in the Delta.
Interagency Ecological Program San Francisco Estuary Larval Entrainment Study (LES)
Fish entrainment into California's State Water Project (SWP) and Central Valley Project (CVP) has been a source of mortality for native osmerid species, including Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys). While entrained adult and juvenile fishes are collected, identified and enumerated, the facilities design does not allow for a quantifiable estimate of larval fishes being entrained. This knowledge gap makes it difficult for managers to make scientifically informed decisions regarding the endangered Longfin & Delta Smelt. The Larval Entrainment Study (LES) aims to address this gap by providing a high-resolution dataset and insights into the variable abundances of Smelt at risk of entrainment, the community composition surrounding them, and associated water quality data. Our study design utilizes a variety of gear types and maximizes replicates to improve the understanding of larval Smelt abundances within the southern reach of the Sacramento and San Joaquin River Delta, the zone of entrainment for the SWP and CVP. Sampling began in 2022 using 10-minute stepped oblique tows of a Smelt Larval Survey (SLS) sled mounted with a 500 μm net. Tows were conducted in West Canal, outside Clifton Court Forebay (CCF), where the risk of entrainment is highest. Sampling was conducted five days a week in 2022 and three days a week in the following years. . Beginning in mid-January 2023, a 940 μm mesh net with the same dimensions as the SLS net was added, with sampling alternating between the two. This provided an intermediate gear between SLS (500 μm) and 20mm (1600 μm) nets. In 2024 we expanded to sample a transect of sites within the Old and Middle River (OMR) corridor. This provides broader spatial resolution and improves our ability to detect Osmerids within the South Delta. Sampling alternated between a high priority day (with intensive sampling in the lower San Joaquin River, SLS stations 809 & 812) and a longer transect day that ran
Interagency Ecological Program San Francisco Estuary Spring Kodiak Trawl Survey 2002 - 2021
The Interagency Ecological Program San Francisco Estuary Spring Kodiak Trawl Survey was initiated by the California Department of Fish and Wildlife (CDFW) in 2002 to improve the detection rate of pre-spawning and mature Delta Smelt (hypomesus transpacificus). The survey began as the Spring Midwater Trawl Survey, an extension of the Fall Midwater Trawl Survey, in 1991 to assist with water management and export decisions in relation to the distribution of pre-spawning Delta Smelt. Net evaluations studies compared the relative catch efficiency of 3 types of nets and found that the Kodiak net was most effective for Sampling adult Delta Smelt. Objectives of SKT are to improve the ability to detect Delta Smelt, obtain maturity status for adult Delta Smelt, and provide results to scientist and managers on a near real-time basis to ais in resource management. SKT operates 6 monthly surveys December through May each lasting 4-5 days in length. Each survey, 40 fix sample locations are sampled using a standard 10 minute Kodiak trawl with a total length of 65 feet and a fully expanded mouth opening of 25 feet by 6 feet. The volume of water sampled is estimated using a General Oceanics flowmeter placed over the side of the boat. The net is constructed of green or black variable mesh ranging in dimension from 2 inches knoteted stretched mesh at the mouth and decreasing by ½ inch through a series of 5 panels to ¼ inch knotless stretched mesh at the cod-end. All fish sampled are identified to species and enumeration, Delta Smelt are staged in the field. At each station, environmental and water quality data are also collected, and include: temperature, electrical conductivity (normalized @ 25°C), water clarity, and tidal condition.
Interagency Ecological Program San Francisco Estuary 20-mm Survey 1995 - 2024
The Interagency Ecological Program San Francisco Estuary 20-mm Survey was initiated by the California Department of Fish and Wildlife (CDFW) in 1995 to monitor the distribution and abundance of post-larval and juvenile Delta Smelt (Hypomesus transpacificus). Delta Smelt are considered to be an annual fish endemic to the upper San Francisco Estuary that spawn in early spring and rear through the summer and fall in fresh to brackish water. Young of the Year (YOY) Delta Smelt are considered juveniles at sizes greater than or equal to 20-mm, and this survey targets those Delta Smelt. The 20-mm Survey currently samples 61 stations at fixed locations from San Pablo Bay through Suisun Bay and into the Sacramento-San Joaquin River Delta every other week from March to July. The survey has historically sampled between 41 and 55 stations. At each station, three 10-minute stepped oblique tows are conducted for fish. Each stepped oblique tow follows a tow schedule to sample the water column up to 32 ft, and the volume of water sampled is estimated using a General Oceanics flowmeter. The net is a cone shaped plankton net composed of 1600μm mesh and measuring 5.5 meters in length with a mouth area of 1.51m2 lashed onto a rigid D-frame with skis. Post-larval and juvenile fish samples are preserved in the field in 10% Formalin dyed with Rose Bengal and brought back to the CDFW Stockton Lab for identification to species and enumeration under a microscope. Fish are measured to fork length or total length when fork is not present. At each station, environmental and water quality data are also collected, and include: top temperature, top and bottom electrical conductivity (normalized at 25 degree C), secchi (cm), surface water clarity (FNU), and tidal condition.
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