Aquatic Ecology Group Active
Tidal Wetlands
Loss of tidal wetland habitat in the San Francisco Estuary affects fish and other aquatic organisms.
Longfin Smelt
Longfin Smelt is a threatened species found in waters along the Pacific coast. Its complex life cycle makes it vulnerable in both freshwater and at sea.
Sacramento Splittail
Spinal deformities in California native fish species, the Sacramento Splittail, are now attributed to exposure to the chemical element selenium.
The California Water Science Center's Aquatic Ecology Group is making great strides in research and reporting.
The Aquatic Ecology Group at the US Geological Survey’s California Water Science Center is a team of scientists working to solve important natural science challenges facing society.
Our research covers all aspects of aquatic ecology with a focus on freshwater, estuarine and marine fishes and environments. Particular topics include:
- Water resources
- Threatened and endangered species
- Fish habitat
- Food web dynamics
- Climate change
- Drought
We work closely with scientists in other disciplines at USGS to tackle challenges with comprehensive, interdisciplinary research. A particular strength of our group is the ability to use new technology to generate novel solutions to natural resource problems. We also maintain active collaborations with many federal, state, and local agencies, and universities.
We pursue innovative solutions to a diverse array of natural resource problems through applied research. A large portion of our research is field-based and incorporates elements of behavioral, population, and community ecology. Individual projects range from the biology and ecology of individual species to the effects of climate change on ecosystems.
Bay-Delta Catchability Study
Santa Ana River Native Fish Study
Hydrologic and Aquatic Ecology Studies at Clear Lake, California
Studying Threatened Fish Species in Clear Lake, CA
Longfin Smelt Distribution in the Coastal Pacific Ocean
Development of a spatially explicit ecosystem model to explore physiochemical drivers of step changes in POD species abundance and distribution in the Sacramento-San Joaquin Delta and Suisun Bay
Mapping Sturgeon Spawning Habitat in the Lower San Joaquin River
Delta sediment measurements to support numerical modeling of turbidity
Modeling in support of development of biocriteria for wadeable California streams and rivers
The role of the alien clam Corbicula fluminea in the regulation of organic carbon in the San Joaquin River watershed
Implementing New Acoustic Monitoring Techniques in the Trinity River
Role Nutrients Play in Fish Death Rates at Rodeo Lagoon
Abundance and Distribution of Fishes in Clear Lake, Lake County, California, 2017-2023
Fish distribution and tidal currents in the Upper San Francisco Estuary, 2022-2023 (ver. 2.0, March 2024)
Post Carr Fire Bioassessment Data, Whiskeytown National Recreation Area, Shasta County, California, 2020
Santa Ana River Native Fish Population and Habitat Data, Santa Ana River, California, 2022
Distribution and stomach contents of fishes in the northern Sacramento-San Joaquin Delta, 2020-2022
Detection range and efficiency of acoustic telemetry receivers in Clear Lake, Lake County, California
Vertical Distribution of Longfin Smelt in the San Francisco Estuary (ver. 2.1, August 2020)
SAR 2018 Native Fish Population and Habitat Study, Santa Ana and San Gabriel Rivers, California
Below are publications associated with the Aquatic Ecology Group
Wetland geomorphology and tidal hydrodynamics drive fine-scale fish community composition and abundance
Physics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary
Etiology of a fish kill, Including the endangered Tidewater Goby (Eucyclogobius newberryi), in a northeastern pacific coastal lagoon
Microhabitat use of native Santa Ana sucker and arroyo chub in an effluent-dominated southern California stream
Hydrodynamics structure plankton communities and interactions in a freshwater tidal estuary
Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta
Joint-species analysis reveals potential displacement of native fishes by non-native fishes within the Santa Ana River, California
Synthesis of data and studies relating to Delta Smelt biology in the San Francisco Estuary, emphasizing water year 2017
Disentangling stationary and dynamic estuarine fish habitat to inform conservation: Species-specific responses to physical habitat and water quality in San Francisco Estuary
Toward improved decision-support tools for Delta Smelt management actions
Eye lenses reveal ontogenetic trophic and habitat shifts in an imperiled fish, Clear Lake hitch (Lavinia exilicauda chi)
Use of the smeltCam as an efficient fish sampling alternative within the San Francisco Estuary
Below are news stories associated with this project.
The following list of partners have helped make the work of the Aquatic Ecology Group possible.
- Overview
The California Water Science Center's Aquatic Ecology Group is making great strides in research and reporting.
The Aquatic Ecology Group at the US Geological Survey’s California Water Science Center is a team of scientists working to solve important natural science challenges facing society.
Our research covers all aspects of aquatic ecology with a focus on freshwater, estuarine and marine fishes and environments. Particular topics include:
- Water resources
- Threatened and endangered species
- Fish habitat
- Food web dynamics
- Climate change
- Drought
We work closely with scientists in other disciplines at USGS to tackle challenges with comprehensive, interdisciplinary research. A particular strength of our group is the ability to use new technology to generate novel solutions to natural resource problems. We also maintain active collaborations with many federal, state, and local agencies, and universities.
- Science
We pursue innovative solutions to a diverse array of natural resource problems through applied research. A large portion of our research is field-based and incorporates elements of behavioral, population, and community ecology. Individual projects range from the biology and ecology of individual species to the effects of climate change on ecosystems.
Filter Total Items: 22Bay-Delta Catchability Study
Addressing Catchability Bias in Fish Surveys San Francisco Bay and the Sacramento-San Joaquin Delta collectively make up the "Bay-Delta." In the scientific study of fish, "catchability" refers to the probability that a fish will be captured by a particular fishing gear or method. Catchability is a measure of how effectively a fishing gear or method can capture fish. "Catch data" refer to...Santa Ana River Native Fish Study
Native Fish Population and Habitat Study, Santa Ana River, California The Santa Ana River, the largest river in southern California, flows through diverse landscapes, from the high desert to urban and suburban areas in Orange, Riverside, and San Bernardino Counties, stretching approximately 96 miles (154 kilometers) from its headwaters in the San Bernardino Mountains to its mouth at the Pacific...Hydrologic and Aquatic Ecology Studies at Clear Lake, California
The USGS California Water Science Center conducts a variety of research activities at Clear Lake, California, including surface-water monitoring and water quality and aquatic habitat studies.Studying Threatened Fish Species in Clear Lake, CA
The Clear Lake Hitch ( Lavinia exilicauda chi ) population, which once flourished in great abundance, has been decimated by loss of spawning habitat, nursery areas, and the encroachment of non-native species. In order to make an informed decision, the California Water Science Center has been asked by the U.S. Fish and Wildlife Service to conduct studies into the fish’s habitat, specifically...Longfin Smelt Distribution in the Coastal Pacific Ocean
Longfin Smelt ( Spirinchus thaleichthys ) is a pelagic fish species found in waters along the Pacific coast, from Alaska to central California. Its complex life cycle makes it vulnerable to threats in both freshwater and at sea. Longfin Smelt is listed as a threatened species by the state of California.Development of a spatially explicit ecosystem model to explore physiochemical drivers of step changes in POD species abundance and distribution in the Sacramento-San Joaquin Delta and Suisun Bay
Prior to 2000, the four most abundant resident pelagic fishes in the study area included two native species, delta smelt (Hypomesus transpacificus) a federal listed endangered species, and longfin smelt (Spirinchus thaleicthys) a state listed endangered species, and two introduced species, threadfin shad (Dorosoma petenense) and age-0 striped bass (Morone saxatilis).Mapping Sturgeon Spawning Habitat in the Lower San Joaquin River
The spawning of adult white sturgeon ( Acipenser transmontanus ) in the lower San Joaquin River was documented recently by the United States Fish and Wildlife Service (USFWS) (Gruber and others, 2012; Jackson and Eenennaam, 2013). Streamflow on the San Joaquin River has been modified by State and Federal water project operations, and there are a variety of questions regarding the effects on fish...Delta sediment measurements to support numerical modeling of turbidity
The purpose of the proposed work is to collect data that will support the development, calibration, and validation of numerical models of sediment transport and turbidity in the Sacramento-San Joaquin Delta.Modeling in support of development of biocriteria for wadeable California streams and rivers
The State Water Resources Control Board (SWRCB) of California has initiated a process to develop biological objectives for wadeable freshwater streams and rivers for the entire state.The role of the alien clam Corbicula fluminea in the regulation of organic carbon in the San Joaquin River watershed
Sources and fate of various forms of organic carbon in the Sacramento-San Joaquin Delta (Delta) and San Joaquin River watershed are of concern because of the importance of identifying the sources of carbon contributing to the oxygen depletion zone on the San Joaquin River near the city of Stockton, the need to understand the causes of the low primary and secondary production in the Delta, and the...Implementing New Acoustic Monitoring Techniques in the Trinity River
Accurate river-sediment data is fundamental to planning and managing river restoration efforts on the Trinity River, and throughout the world’s waterways. The USGS has developed a “hydrophone” that enables scientists to listen to sediment particles as they move along the riverbed in order to inexpensively and reliably record near-continuous sediment-bedload-transport data. For this study...Role Nutrients Play in Fish Death Rates at Rodeo Lagoon
Scientists investigate excessive nutients levels in Rodeo Lagoon that are believed to be cause of dying fish - Data
Abundance and Distribution of Fishes in Clear Lake, Lake County, California, 2017-2023
Field data for fishes sampled using bottom and surface gill nets during daylight hours in Clear Lake, California, USA. This data release includes all measured environmental parameters and fish taxa included in the analysis. First posted - December 20, 2018 (available from author) Revision - November 26, 2019 (available from author) Revision - January 21, 2022 (available from author) Revision - OcFish distribution and tidal currents in the Upper San Francisco Estuary, 2022-2023 (ver. 2.0, March 2024)
This data release includes field data for fishes sampled through mid-water trawls and otter trawl methods from Suisun Bay, California to the mouth of the Sacramento River. These data were collected from the months of September through October in 2022 and 2023 as a part of a multi-year study of Suisun Dredging and Fish Distribution (SDFD). This data release includes quantitative data on collected fPost Carr Fire Bioassessment Data, Whiskeytown National Recreation Area, Shasta County, California, 2020
This data release contains data collected during August 2020 for the post Carr fire Bioassessment project at Whiskeytown National Recreation Area, Shasta County, California. Data includes sediment and habitat characteristics, water chemistry, and biological conditions of tributaries to Whiskeytown Lake and Clear Creek below the dam. Samples were also collected to assess concentrations of metals inSanta Ana River Native Fish Population and Habitat Data, Santa Ana River, California, 2022
This dataset includes 2022 reach fish data and reach habitat data collected to support development of the upper Santa Ana River Habitat Conservation Plan for the Santa Ana Sucker (Catostomus santaanae) and the Arroyo Chub (Gila orcutti) in the Santa Ana River, California.Distribution and stomach contents of fishes in the northern Sacramento-San Joaquin Delta, 2020-2022
This data set includes count, location, and ancillary habitat data for fishes sampled in adjacent reaches of Georgiana Slough, Sacramento River, and Steamboat Slough in the northern Sacramento-San Joaquin Delta. It also includes data on the stomach contents of selected individual black basses (Micropterus). Fishes were sampled by boat electrofishing from approximately January-May, 2020-2022, plusDetection range and efficiency of acoustic telemetry receivers in Clear Lake, Lake County, California
Data on the detection range and efficiency of VR2W-69 kHz acoustic receivers (Innovasea Marine Systems Canada Inc., Bedford, Nova Scotia, Canada; https://www.vemco.com/) were collected to guide the development of telemetry studies of the Clear Lake Hitch (Lavinia exilicauda chi), an imperiled fish species endemic to Clear Lake, Lake County, California. The study took place June 21, 2021 through JuVertical Distribution of Longfin Smelt in the San Francisco Estuary (ver. 2.1, August 2020)
Field data for fishes sampled using mid-water trawls, otter trawls, and the SmeltCam during day and night in San Pablo Bay, CA. This data release includes all measured environmental parameters and fish taxa included in the analysis.SAR 2018 Native Fish Population and Habitat Study, Santa Ana and San Gabriel Rivers, California
This dataset includes 2018 reach fish data and reach habitat data collected to support development of the upper Santa Ana River Habitat Conservation Plan for the Santa Ana Sucker (Catostomus santaanae) and the Arroyo Chub (Gila orcutti) in the Santa Ana and San Gabriel Rivers, California. - Publications
Below are publications associated with the Aquatic Ecology Group
Filter Total Items: 35Wetland geomorphology and tidal hydrodynamics drive fine-scale fish community composition and abundance
Effective restoration of tidal wetlands for fish communities requires clear goals and mechanistic understanding of the ecosystem drivers which affect fish distribution and abundance. We examined fish community responses to abiotic habitat features in two adjacent but dissimilar freshwater tidal wetlands in the Sacramento-San Joaquin Delta, CA, USA, each of which represents a potential restorationAuthorsJustin Kinsey Clause, Mary Jade Farruggia, Frederick V. Feyrer, Matthew J. YoungPhysics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary
Executive SummaryThe Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of ReclamatiAuthorsLarry R. Brown, David E. Ayers, Brian A. Bergamaschi, Jon R. Burau, Evan T. Dailey, Bryan D. Downing, Maureen A. Downing-Kunz, Frederick V. Feyrer, Brock M. Huntsman, Tamara E. C. Kraus, Tara Morgan, Jessica R. Lacy, Francis Parchaso, Catherine A. Ruhl, Elizabeth B. Stumpner, Paul Stumpner, Janet Thompson, Matthew J. YoungEtiology of a fish kill, Including the endangered Tidewater Goby (Eucyclogobius newberryi), in a northeastern pacific coastal lagoon
Ecological disturbances such as fish kills can negatively impact ecosystem processes in coastal lagoons. To gain an understanding of factors causing fish kills, we examined conditions associated with a summertime fish kill in a northeastern Pacific coastal lagoon (Rodeo Lagoon, CA, USA). Examination of available data indicated the fish kill was likely caused by hypoxia involving the following etioAuthorsFrederick V. Feyrer, Matthew J. Young, Tamara E. C. Kraus, Elizabeth B. Stumpner, Darren Fong, Kurt D. CarpenterMicrohabitat use of native Santa Ana sucker and arroyo chub in an effluent-dominated southern California stream
A significant amount of the base flow of the Santa Ana River, located within California's arid Los Angeles metropolitan region, originates from two wastewater treatment facilities: the Rialto wastewater treatment facility and Rapid Infiltration and Extraction facility. The Santa Ana sucker (Pantosteus santaanae, syn. Catostomus santaanae) and arroyo chub (Gila orcuttii) are two native species listAuthorsBrock Huntsman, Larry R. Brown, Jason May, Kai Palenscar, Kerwin Russell, Heather Dyer, Marissa L. Wulff, Brett Mills, Chris JonesHydrodynamics structure plankton communities and interactions in a freshwater tidal estuary
Drivers of phytoplankton and zooplankton dynamics vary spatially and temporally in estuaries due to variation in hydrodynamic exchange and residence time, complicating efforts to understand controls on food web productivity. We conducted approximately monthly (2012–2019; n = 74) longitudinal sampling at 10 fixed stations along a freshwater tidal terminal channel in the San Francisco Estuary, CalifAuthorsAdrianne P Smits, Luke C. Loken, Erwin E Van Nieuwenhuyse, Matthew J. Young, Paul Stumpner, Leah Kammel, Jon R. Burau, Randy A Dahlgren, Tiffany Brown, April Hennessey, Steven SadroHydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta
Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are a defining feature in tidal terminal channel ecosystems from which native aquatic communities have evolved. However, few studies have explored the relationship between fish community structure and hydrodynamics in these tidal terAuthorsBrock Huntsman, Matthew J. Young, Frederick V. Feyrer, Paul Stumpner, Larry R. Brown, Jon R. BurauJoint-species analysis reveals potential displacement of native fishes by non-native fishes within the Santa Ana River, California
Accurate estimates of abundance are a cornerstone for resource managers to make effective decisions for fish conservation. However, multiple sampling methods often are required to sample fish communities, and ignoring the detection process can create substantial bias in latent state parameter estimation (e.g., abundance, survival). We developed a joint-species N-mixture model that integrated snorkAuthorsBrock Huntsman, Larry R. Brown, Kai Palenscar, Chris Jones, Kerwin Russell, Heather Dyer, Brett Mills, Marissa L. Wulff, Jason MaySynthesis of data and studies relating to Delta Smelt biology in the San Francisco Estuary, emphasizing water year 2017
In the San Francisco Estuary (SFE), the effects of freshwater flow on the aquatic ecosystem have been studied extensively over the years and remains a contentious management issue. It is especially contentious with regards to the Delta Smelt (Hypomesus transpacificus), a species endemic to the SFE that has been listed as threatened under the Federal Endangered Species Act and endangered by the StaAuthorsShawn Acuna, Randy Baxter, Aaron J. Bever, Larry R. Brown, Christina Burdi, Gonzalo Castillo, Louise Conrad, Steven Culberson, Lauren Damon, Jared Frantzich, Lenny Grimaldo, Bruce Hammock, April Hennessy, James A. Hobbs, Shruti Khanna, Peggy W. Lehman, Michael L. MacWilliams, Brian Mahardja, Andrew A. Schultz, Steven B. Slater, Ted Sommer, Swee Teh, Janet ThompsonDisentangling stationary and dynamic estuarine fish habitat to inform conservation: Species-specific responses to physical habitat and water quality in San Francisco Estuary
Estuaries represent critical aquatic habitat that connects surface water distributed between Earth’s landmasses and oceans. They are dynamic transitional ecosystems, which provide important habitat for fishes and other aquatic organisms. Effective conservation of species inhabiting estuaries requires knowledge of the habitat features that drive their abundance and distribution. We sought to elucidAuthorsFrederick V. Feyrer, Matthew J. Young, Brock Huntsman, Larry R. BrownToward improved decision-support tools for Delta Smelt management actions
The Collaborative Science and Adaptive Management Program (CSAMP) has endorsed a goal of reversing the recent downward trajectory of the Delta Smelt population within 5-10 generations, with the long-term aim of establishing a self-sustaining population. An ambitious agenda of management actions is planned, and more management actions are being considered. This White Paper furthers one of the recomAuthorsDenise Reed, Shawn Acuna, Eli Ateljevich, Larry R. Brown, Ben Geske, Edward Gross, Jim Hobbs, Wim J. Kimmerer, Lisa Lucas, Matthew Nobriga, Kenneth A RoseEye lenses reveal ontogenetic trophic and habitat shifts in an imperiled fish, Clear Lake hitch (Lavinia exilicauda chi)
Stable isotopes recorded in fish eye lenses are an emerging tool to track dietary shifts coincident with use of diverse habitats over the lifetime of individuals. Eye lenses are metabolically inert, sequentially deposited, archival tissues that can open avenues to chronicle contaminant exposures, diet histories, trophic dynamics and migratory histories of individual fishes. In this study, we demonAuthorsMatthew J. Young, Veronica Larwood, Justin Kinsey Clause, Miranda Bell-Tilcock, George Whitman, Rachel C. Johnson, Frederick V. FeyrerUse of the smeltCam as an efficient fish sampling alternative within the San Francisco Estuary
Resource managers often rely on long-term monitoring surveys to detect trends in biological data. However, no survey gear is 100% efficient, and many sources of bias can be responsible for detecting or not detecting biological trends. The SmeltCam is an imaging apparatus developed as a potential sampling alternative to long-term trawling gear surveys within the San Francisco Estuary, California, tAuthorsBrock Huntsman, Frederick V. Feyrer, Matthew J. Young - News
Below are news stories associated with this project.
- Partners
The following list of partners have helped make the work of the Aquatic Ecology Group possible.