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Fish abundance in the San Francisco Estuary (1959-2024), an integration of 10 monitoring surveys.
The San Francisco Estuary (SFE) is simultaneously a central hub of water delivery in California and home to commercially important and endangered fishes, such as Chinook Salmon, Green Sturgeon, and Delta and Longfin Smelt. Extensive ecological monitoring has been conducted for over 50 years, mainly under the auspices of the Interagency Ecological Program for the San Francisco Estuary (https://iep.ca.gov/). We integrated fish catch and length data from 10 long-term monitoring surveys in the SFE. The integrated database contains survey-level data such as environmental variables and sampling effort in addition to the fish-level species, lengths, and counts. Zero catches have been filled in for any species not caught in a sample. The geographic scope includes San Francisco Bay through the upper estuary, and the timeseries spans 1959 to 2024. Sampling methods, gear, fish length metric, and other factors differ among the component surveys. Sampling designs (locations and temporal frequency) have also changed over time. Thus, it is highly recommended to inspect the documentation of the component surveys for more information on their methods.
CALCOFI fish larvae at 66 standard stations, 1966 - ongoing
The fish larvae (ichthyoplankton) survey is conducted through the California Cooperative Fisheries Investigations program (CALCOFI, http://www.calcofi.org/). These data are a time series of fish larvae counts (or density, as number per 10 square meter of ocean surface) collected in the area of the California Current between San Diego and Avila Beach, California. Original data were filtered to facilitate consistent comparisons over time and space. The original CalCOFI fish larvae count data is available from the CoastWatch West Coast Regional Node (WCRN) at NOAA’s Pacific Fisheries Environmental Laboratory, http://coastwatch.pfeg.noaa.gov/erddap/tabledap/index.html. The dataset presented here is an aggregation of 31 data files, originally divided alphabetically by taxon (named “CalCOFI Larvae Counts, Scientific Names * to *”). The data were filtered to include only the 66 core stations with a maximum of 1 cruise per season. These 66 core stations have been most frequently sampled in the past and sampling is ongoing. CalCOFI sampling began in 1949. However, the dataset presented here begins in 1966 to include only samples that were analyzed with techniques that apply the most current and accurate identification of larvae to the species level. As the backlog of samples (i.e., before 1966) is re-examined, this dataset will be augmented with that additional, earlier data.
2021-2022 West False River Emergency Drought Barrier water quality, flow, and fish monitoring
To manage the critically low 2021 water supply for beneficial uses, DWR installed the temporary emergency drought barrier (EDB) on West False River in the Sacramento–San Joaquin Delta (Delta), approximately 5 miles south of Rio Vista, California, in Contra Costa County in June 2021. To monitor the effectiveness and impacts of the EBD, a monitoring program was initiated to track changes in hydrodynamics, water quality, fish, harmful algal blooms, and aquatic weeds in the vicinity of the EDB. The EDB was left in place during the winter of 2021-2022 and removed in fall of 2022. This data set includes all data collected as part of that monitoring program and subsets of ongoing monitoring programs that were used in the final effectiveness report for the EDB.
Interagency Ecological Program: Discrete water quality and phytoplankton data from the Sacramento River floodplain and Yolo Bypass tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998 - 2022
The Yolo Bypass Fish Monitoring Program (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. YBFMP staff also conduct analyses of YBFMP monitoring data to address pertinent management related questions as identified by IEP. The Yolo Bypass has been identified as a high restoration priority by the National Marine Fisheries Service and US Fish and Wildlife Service Biological Opinions for Delta Smelt, Winter and Spring-run Chinook salmon and by California EcoRestore. The YBFMP informs the restoration actions that are mandated or recommended in these plans and provides critical baseline data on the ecology of the bypass and how it interacts with the broader San Francisco Estuary. Program objectives include: Collecting baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance; Analyzing and communicating Yolo Bypass data with stakeholders and the scientific and management communities to address pertinent management related questions; Providing technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. We collect discrete water quality data using a YSI ProDSS and sample phytoplankton, chlorophyll and nutrients as discrete water grabs taken biweekly (or weekly during Yolo Bypass inundation) along with lower trophic tows. Water is sampled at three sites along the Yolo Bypass and Sacramento River, then processed and analyzed by an internal DWR laboratory.
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
UC Davis Suisun Marsh Fish Study, CA,1980-2024
Suisun Marsh, at the geographic center of the northern San Francisco Estuary, provides important habitat for native and non-native fishes, as well as many valued and endangered plants, reptiles, mammals, and birds. The University of California, Davis, Suisun Marsh Fish Study, in partnership with the California Department of Water Resources (DWR), has systematically monitored the marsh's fish populations since January 1980 (O'Rear et al. 2023). The study’s main purpose has been to determine natural and human-caused factors affecting fish and invertebrate distribution and abundance. All sampling has occurred in Suisun Marsh, mostly in subtidal sloughs. Sampling began in 1979, but standardized methods and stations were not implemented until 1980. Sampling has occurred monthly from January 1980 to the present at geographically fixed stations. Fixed stations have been necessary because snags preclude uninterrupted trawls in many sections of smaller sloughs. Originally, 48 stations were selected haphazardly that could be easily and safely sampled by boat and covered the breadth of Suisun Marsh to ensure capture of all variability in fish populations. However, the emphasis has been on sampling smaller sloughs because they exhibit greater variability in a smaller space than the marsh's two big sloughs (Suisun and Montezuma), and because only the big sloughs are sampled by other long-term monitoring projects such as California Fish and Wildlife's Fall Midwater Trawl. The 48 stations were sampled in 1980 and 1981. Water quality and catches were then compared across these stations to locate redundancies and thereby improve logistical efficiency while maximizing capture of variation by eliminating uninformative stations (Brown et al. 1981). Seventeen stations were then chosen and were continuously sampled from 1980 through 1993. Geographic scope was reassessed in 1994, when sampling was reinitiated in the northeast marsh in Denverton and Nurse sloughs at four stations (DV2, DV3
Interagency Ecological Program: Fish catch and associated water quality for the Fall Midwater Trawl Survey, Sacramento-San Joaquin Delta, 1967-2024
The Interagency Ecological Program’s (IEP) Fall Midwater Trawl Survey (FMWT) is a long-term monitoring survey conducted by the California Department of Fish and Wildlife (CDFW) and has sampled annually since its inception in 1967, with the exceptions of 1974 and 1979, when sampling was not conducted. The FMWT was initiated to determine the relative abundance and distribution of age-0 Striped Bass (Morone saxatilis) in the San Francisco Estuary (California, United States), but the data has also been used for other upper estuary pelagic species, including Delta Smelt (Hypomesus transpacificus), Longfin Smelt (Spirinchus thaleichthys), American Shad (Alosa sapidissima), Splittail (Pogonichthys macrolepidotus), and Threadfin Shad (Dorosoma petenense). The FMWT currently samples 130 stations each month from September to December and a subset of this data is used to calculate an annual abundance index. These 130 stations range from San Pablo Bay upstream to Stockton on the San Joaquin River, and West Sacramento on the Sacramento Deep Water Ship Channel. FMWT sampling data includes 193 unique station locations throughout the San Francisco Estuary; 63 are not currently sampled. Most stations no longer sampled occur in South and Central San Francisco Bay (1968-1979), with others located in San Pablo Bay and upstream into the Delta. There are catch records for stations that were sampled only once. Data users are encouraged to look at station frequency over time to understand when and where sampling occurred. Sampling takes approximately 14 days per month to complete. Historically, FMWT sampling occasionally began as early as July (1972) or August (1968-1973, 1993-1994, 1996-1997) and sometimes continued past December to March (1968-1973, 1978, 1991-2001) or beyond (1992-1995). The Spring Midwater Trawl (SMWT) was a modified survey created to continue sampling January-March to track movements of mature adult delta smelt from 1991-2001. SMWT was replaced in 2002 with the more e
Interagency Ecological Program and US Fish and Wildlife Service: Beach Seine Efficiency Study, collected by the Delta Juvenile Fish Monitoring Program, 2013-2018
Within the San Francisco Estuary, beach seining has been used since the 1970s by the U.S. Fish and Wildlife Service's Delta Juvenile Fish Monitoring Program (DJFMP) to monitor the relative abundance and distribution of juvenile Chinook salmon and other fishes of management concern occurring in near shore habitats. Over 2,000 seine samples are currently being collected throughout the San Francisco Estuary annually. Data from these surveys are used to make various water operation decisions and help inform managers on the status of fish populations within the San Francisco Estuary. By not accounting for the variability of species- and size-specific efficiency of beach seines across environmental gradients, the metrics developed by the DJFMP are likely underestimated and biased to an unknown extent. Consequently, the ability of the DJFMP to document the true occupancy of fishes for water operations and population vicissitude may be inhibited. Therefore, the first objective of this study is to estimate the species- and size-specific capture efficiency of DJFMP beach seines for fishes occurring in near shore habitats within the San Francisco Estuary. The second objective is to model the observed efficiency estimates using habitat variables to allow managers to account for incomplete detection when estimating fish abundance and occupancy from DJFMP beach seine data.
Qualitative Larval Fish Sampling at the California Department of Water Resource’s State Water Project
The California Department of Water Resource’s State Water Project utilizes the John E. Skinner Delta Fish Protective Facility (Skinner Fish Facility) to salvage fishes that would otherwise become entrained during operations to divert water from the Sacramento-San Joaquin River Delta (Delta). Water is diverted from the Delta to meet California’s agricultural, municipal, industrial, and environmental needs. The Skinner Fish Facility, located in Contra Costa County and situated ahead of the Harvey O. Banks Pumping Plant, began salvaging fish in 1968 but historically, only recorded fork length measurements for fish greater than 20 millimeters. Beginning in 2009, the Skinner Fish Facility implemented qualitative larval sampling in response to the 2008 U.S. Fish and Wildlife Service Biological Opinion on the coordinated operations of the Central Valley Project (CVP) and State Water Project (SWP). This entailed collecting, retaining, and identifying larval fishes to better understand SWP impacts on Delta Smelt. Qualitative larval sampling took place annually from 2009 through 2025, during the Old and Middle River management period and based upon Delta Smelt spawning (typically mid-February to June). The California Department of Water Resources collected and processed samples from 2020 through 2025. Data from 2009 through 2019 were processed and retained by others and are not included in this dataset.
Interagency Ecological Program: San Francisco Bay Study Survey for Fish and Mobile Crustaceans 1980-2024
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 (brachyuran crabs and caridean shrimp) in the San Francisco Estuary, mainly downstream of the Sacramento-San Joaquin Delta. The Bay Study survey currently samples 52 open-water stations monthly from a research vessel with two types of trawl gear: a midwater trawl to sample pelagic fishes, and an otter trawl to sample demersal fishes, crabs, and shrimp. Historically, the study also included plankton sampling (1980-1989) for larval fish and crustaceans. Fish collected by the otter and midwater trawl are identified to species, counted, and a representative subsample is measured. In addition, crabs from the otter trawl are identified, counted, sexed, and measured, and gelatinous zooplankton from the midwater trawl are identified and counted. Shrimp are retained from each otter trawl sample and returned to the laboratory for processing, which includes identification, counts, sex, and length. Additional data collected at each station includes water depth, Secchi, and a water column profile of temperature and conductivity. This data publication includes fish, crab, shrimp, gelatinous zooplankton (jellies), and water quality data. Metadata related to the plankton sampling will be included in the future when this data is published.
Analyzing fish leaping and movement potential at a migratory barriers: Michigan 2022-2025
The enclosed Matlab scripts and supporting files are used for fish passage assessments at small migratory barriers with complex geometry. Building upon a 2-D ballistic trajectory mathematical model, the model incorporates field-derived behavioral parameters and simulated flow data to evaluate the likelihood of successful leaping attempts. The model integrates stochastic variation in key fish characteristics—such as body length, launch speed, and leap origin—to simulate a range of realistic leaping scenarios. These are coupled with three-dimensional, CFD-derived inputs for local water velocity and depth, enabling a spatially detailed assessment of hydraulic conditions that are most conducive to successful passage. This integrated approach provides a more comprehensive and biologically informed evaluation of passage potential at migratory barriers. To demonstrate its utility, the model is applied in a case study examining the influence of complex barrier geometry on fish passage outcomes, highlighting its potential to inform engineering design decisions that either facilitate or limit fish movement based on management objectives. The enclosed files are associated with steelhead passage at a arc-labyrinth and low-flow weir at the FishPass project, located on the Boardman/Ottaway River, MI, USA.
Fish Restoration Program Tidal Wetland Restoration Monitoring in Upper San Francisco Estuary, 2015-ongoing
The Fish Restoration Program Monitoring Team assesses the biological effectiveness of 8,000+ acres of tidal wetland restoration in the Upper San Francisco Estuary (Sacramento-San Joaquin Delta and Suisun Marsh) through a contract with the CA Department of Water Resources. The restoration is pursuant to requirements in the 2008/2009 and 2019 Biological Opinions for state and federal water project operations. Data on fish and invertebrate abundance on or near these sites was collected as baseline monitoring data and to determine the most efficient methods for monitoring wetlands. Understanding how invertebrate, fish, and phytoplankton communities change pre- to post-restoration is essential to evaluating the benefits of tidal wetlands to native fish species. Invertebrate data was collected using sweep nets, benthic cores, neuston nets, and zooplankton trawls. Fish data was collected using otter trawls, lampara nets, and beach seines. For each method, the team recorded the catch of fish, invertebrates, and other organisms, length of selected organisms, and a suite of environmental information, including: dissolved oxygen, water temperature, pH, specific conductance, turbidity, chlorophyll a, phycocyanin, and dissolved organic carbon. Additional water quality samples, processed for Chlorophyll a, Dissolved Ammonia, Dissolved Nitrite + Nitrate, Dissolved Organic Carbon, Dissolved Organic Nitrogen, Dissolved Ortho-phosphate, Pheophytin a, Total Kjeldahl Nitrogen, Total Organic Carbon, Total Phosphorus, and Total Suspended Solids, were collected at a subset of sampling sites. Data are collected before and after restoration at project and reference sites (Before-After-Control-Impact-design), as well as at adjacent water bodies.
CFP01 Fish population on selected watersheds at Konza Prairie (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-knz/87/8. The abstract below was extracted from the Level 0 data package and is included for context: Fishes were collected by habitat (pool or riffle) at 6 sites in the Kings Creek watershed with a single-pass electrofishing survey with one person operating the electrofisher and two people dipnetting. Collections were made seasonally.
Darwin Core Archive: Santa Barbara Channel fish surveys at deep reefs: Footprint, Piggy Bank, Anacapa Passage
The dataset contains fish surveys from deep natural reefs in the northern Santa Barbara Channel Islands, Southern California, mainly at reefs named Piggy Bank, Footprint (local names) and Anacapa Passage. Data collection began in 1995. Reefs are located at depths between 30 and 360 m (100 and 1,180 feet). Sampling was by the manned submersibles Delta and DualDeepworker and an unmanned Remotely Operated Vehicle (ROV). These sites included a wide range of such habitats as banks, ridges, and carbonate reefs, ranging in size from a few kilometers in length to less than a hectare in area. On these features, we focused on hard bottom macrohabitats, including kelp beds, boulder and cobble fields, and bedrock outcrops. Transects were not deliberately revisited; some reefs were surveyed as many as four times per year. All transects are 2 m wide; transect length varied (see data). Fishes were identified to lowest possible taxon (usually species), and verified against the WoRMs database (http://www.marinespecies.org/). This dataset is formatted as a Darwin Core Archive (DwC-A, occurrence core). This is a derived data product and see provenance for the source data.
Darwin Core Archive: Santa Barbara Channel fish surveys at shallow outcrops
Nine nearshore, shallow-water rock outcrops, seven along the mainland and two off Anacapa Island, were monitored annually from 1995 to 2000. All locations were surveyed using scuba, and belt transects was were conducted at each site. These natural outcrops are geographically distributed across the Santa Barbara Channel providing opportunities for spatial and temporal comparisons between natural reef and oil/gas platforms. Fish surveys at platforms were conducted using scuba within a few days of these surveys at rock outcrops; the data can be viewed at: <link xlink:href="https://portal.lternet.edu/nis/mapbrowse?scope=edi&identifier=113">https://portal.lternet.edu/nis/mapbrowse?scope=edi&identifier=113</link> This scuba project was conducted and reported under a cooperative agreement (Agreement 1445-CA09-95-0836) between the U. S. Geological Survey (Biological Resources Division) and the University of California, Santa Barbara. Citation of report: Love, M. S., D. M. Schroeder, and M. M. Nishimoto. 2003. The ecological role of oil and gas production platforms and natural outcrops on fishes in southern and central California: a synthesis of information. U. S. Department of the Interior, U. S. Geological Survey, Biological Resources Division, Seattle, Washington, 98104, OCS Study MMS 2003-032. <link xlink:href="http://www.lovelab.id.ucsb.edu/Report.pdf">http://www.lovelab.id.ucsb.edu/Report.pdf</link>
Darwin Core Archive: Santa Barbara Channel fish surveys at shallow regions of oil and gas platforms (SCUBA)
This dataset included fish counts that were surveyed in the shallow sections (0 – 40 meters) of the oil and gas platforms using Scuba. The oil and gas platforms are located in the Santa Barbara Channel, California, USA. Each of the eleven platforms (GILDA, GINA, HOLLY, IRENE, HERMOSA, HIDALGO, GAIL, GRACE, HARVEST, C, and HENRY) were surveyed multiple times a year from 1995 to 2000. This scuba project was conducted and reported under a cooperative agreement (Agreement 1445-CA09-95-0836) between the U. S. Geological Survey (Biological Resources Division) and the University of California, Santa Barbara. This dataset is formatted as a Darwin Core Archive (DwC-A, occurrence core). This is a derived data product and see provenance for the source data. Citation of report: Love, M. S., D. M. Schroeder, and M. M. Nishimoto. 2003. The ecological role of oil and gas production platforms and natural outcrops on fishes in southern and central California: a synthesis of information. U. S. Department of the Interior, U. S. Geological Survey, Biological Resources Division, Seattle, Washington, 98104, OCS Study MMS 2003-032. http://www.lovelab.id.ucsb.edu/Report.pdf These fish surveys at platforms were conducted within a few days of surveys at rock outcrops, which can be viewed at: https://portal.edirepository.org/nis/mapbrowse?scope=edi&identifier=112 The deeper sections of the oil platform were surveyed using the research submarine Delta; the data can be viewed at: https://portal. edirepository.edu/nis/mapbrowse?scope=edi&identifier=111
UCSB SONGS Mitigation Monitoring: Wetland Performance Standard - Fish Abundance and Species Richness
These data describe the annual estimates of density of wetland fish (all species combined) and the species richness (as the number of unique species) in six main channel and six tidal creek locations at four coastal wetlands as part of the SONGS San Dieguito Wetland Restoration monitoring program to track long-term patterns in species abundance and diversity. This study began in 2012 in the San Dieguito Wetland in San Diego County, CA, Carpinteria Salt Marsh in Santa Barbara County, CA, and Mugu Lagoon in Ventura County, CA. Tijuana Estuary in San Diego County was added in 2013. Beginning in 2024, Tijuana Estuary was replaced with Los Penasquitos Lagoon in San Diego County, CA.
UCSB SONGS Mitigation Monitoring: Reef Performance Standard - Fish Standing Stock
These data describe annual estimates of fish standing stock (in tons) supported by the artificial reef, Wheeler North Reef, in Orange County, CA (33.40210N, 117.62420W). Data collection began in 2009 to evaluate the ability of Wheeler North Reef to compensate for losses of kelp forest habitat and associated biota caused by the operation of the San Onofre Nuclear Generating Station (SONGS).
UCSB SONGS Mitigation Monitoring: Reef Performance Standard - Fish Abundance and Richness
These data describe annual estimates of the density and species richness (evaluated as species density) of young-of-year (less than 1 year old) and resident (greater than 1 year old) reef fish from replicate transects at three subtidal reefs. Data collection began in 2009 at an artificial reef (Wheeler North Reef in Orange County, CA) and two natural reference reefs (San Mateo Kelp in Orange County, CA and Barn Kelp in San Diego County, CA) to evaluate the ability of Wheeler North Reef to compensate for losses of kelp forest habitat and associated biota caused by the operation of San Onofre Nuclear Generating Station (SONGS).
Fish and crayfish density and count data for Peeks Creek, Macon County, NC, USA 2005-2014, 2019, and 2022 following a catastrophic debris flow, as well as six reference streams
We followed the process of recovery of the fish and crayfish assemblage in Peeks Creek, a high-gradient second order stream in the Little Tennessee River watershed of North Carolina, after a debris flow devastated the channel and its riparian zone. After 15 years, the fish assemblage had recovered, and the channel and riparian zone had stabilized. Of the three major components of the fish assemblage, Rainbow Trout (Oncorhynchus mykiss (Walbaum)), a strong swimmer, reappeared in year 1. Longnose Dace (Rhinichthys cataractae (Valenciennes in Cuvier and Valenciennes)) reappeared in year 3. Mottled Sculpin (Cottus bairdii Girard), a weak swimmer, did not become established until year 6 and only resumed expected abundance in year 9. Appalachian Brook Crayfish (Cambarus bartonii cavatus Hay) numbers recovered quickly, though only one individual was found the year following the debris flow. Unassisted natural recovery occurred after a costly engineered restoration project had been rejected and arguably represents the preferable solution. However, recovery of the fish assemblage may not have been achieved if the stream flowed directly into an impoundment or low gradient river that lacked the source of species for recolonization, or if the stream had been located above a barrier to upstream movement.
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