Science and Products
Aquatic Ecology Group
The California Water Science Center's Aquatic Ecology Group is making great strides in research and reporting.
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).
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...
Development of Numeric Flow Criteria to Support Freshwater Biological Objectives and Hydrologic Modification Management in California's Wadeable Streams
The State Water Resources Control Board (SWRCB) of California has initiated a process to develop numerical biological objectives for wadeable freshwater streams and rivers for the entire state. Use of biological endpoints for regulatory or compliance purposes requires the ability to relate specific stressors to key biological metrics and to use this understanding to influence management actions...
Whiskeytown Aquatic Inventory Assessment
The project focuses on the assessment of aquatic biology, habitat, and water quality conditions of the major WHIS watersheds
Estimating Natural Flows for Hydrologic Reference Streams
Scientists develop metrics of expected hydrological conditions at ungaged sites throughout Callifornia
Application of the SmeltCam to Describe Processes Influencing Delta Smelt Distribution and Movements
The California Water Science Center's "SmeltCam" helps describe processes influencing Delta Smelt distribution and movement.
Native Fish Population and Habitat Study - Santa Ana River
California Water Science Center scientists further research on two native fish species.
Exploring Drivers of Pelagic Fish Population Decline in Bay-Delta
USGS scientists develop spatially explicit ecosystem model to explore changes pelagic fish species population and distribution in the Sacramento-San Joaquin Delta and Suisun Bay.
Ecology of Selected Tidal Wetlands of the San Francisco Estuary
Researachers study differences of tidal marsh restoration efforts throughout Bay-Delta ecosystem.
Santa Ana River Native Fish Population and Habitat Data, Santa Ana River, California, 2020
This dataset includes 2020 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.
Data used in projected flow analysis in Yolo Bypass under 20 scenarios of climate change
Yolo Bypass is an ecological feature of the Bay-Delta ecosystem in California that provides floodplain habitat for spawning and rearing of Sacramento Splittail (Pogonichthys macrolepidotus) and rearing of juvenile Chinook Salmon (Oncorhynchus tshawytscha) when inundated. We used outputs from 10 climate change models for two Representative Concentration Pathways (RCPs) for greenhouse gas concentrat
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.
SAR 2019 Native Fish Population and Habitat Study, Santa Ana River, California
This dataset includes 2019 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.
SAR 2017 Native Fish Population and Habitat Study, Santa Ana River, California
This dataset includes: 1) microhabitat use data for fish 100 mm and larger; 2) reach fish data; and 3) reach habitat data for the Santa Ana Sucker (Catostomus santaanae) and the Arroyo Chub (Gila orcutti) in the Santa Ana River, California. Habitat availability data was not collected in 2017.
SAR 2016 Native Fish Population and Habitat Study, Santa Ana River, California
Data included in this dataset include: 1) population estimate data; 2) microhabitat use data; and 3) microhabitat availability data for the Santa Ana Sucker (Catostomus santaanae) and the Arroyo Chub (Gila orcutti) in the Santa Ana River, California.
Filter Total Items: 115
Hydrodynamics 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 ter
Chapter 1: General conceptual model for climate change in the Upper San Francisco Estuary
This report is a collaboration by many state and federal agencies working in the Upper San Francisco Estuary to analyze the potential impacts of climate change to different ecosystems found here. Management stategies for ecological values in the face of climate change require reliable and focused information. In this technical report, our focus is on the Upper San Francisco Estuary (SFE), which co
Floodplains and climate change
Floodplains are landscape features that are periodically inundated by water from adjacent rivers (Opperman et al. 2010). Ecologically, functional floodplains are characterized by three primary elements: connectivity, flow regime, and spatial scale. Water quantity flowing over floodplains can vary greatly. Based on a flood’s effects on the floodplain, three flood categories have been defined: flood
Warming in the upper San Francisco Estuary: Patterns of water temperature change from five decades of data
Temperature is a key controlling variable from subcellular to ecosystem scales. Thus, climatic warming is expected to have broad impacts, especially in economically and ecologically valuable systems such as estuaries. The heavily managed upper San Francisco Estuary supplies water to millions of people and is home to fish species of high conservation, commercial, and recreational interest. Despite
Climate change and fishes in estuaries
This chapter provides an overview of the main drivers of change in estuarine systems, their expected causes and impacts on estuarine fish and fisheries. An analysis of global, regional and local patterns of estuarine fish and how climate-induced change may impact estuarine systems and their fish communities is provided. We also examine the main environmental, climatic and biological stressors like
Joint-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 snork
Synthesis 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 Sta
Disentangling 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 elucid
Toward 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 recom
Resistance and resilience of pelagic and littoral fishes to drought in the San Francisco Estuary
Many estuarine ecosystems and the fish communities that inhabit them have undergone substantial changes in the past several decades, largely due to multiple interacting stressors that are often of anthropogenic origin. Few are more impactful than droughts, which are predicted to increase in both frequency and severity with climate change. In this study, we examined over five decades of fish monito
Hydrodynamics drive pelagic communities and food web structure in a tidal environment
Hydrodynamic processes can lead to the accumulation and/or dispersal of water column constituents, including sediment, phytoplankton, and particulate detritus. Using a combination of field observations and stable isotope tracing tools, we identified how hydrodynamic processes influenced physical habitat, pelagic communities, and food web structure in a freshwater tidal system. The pelagic habitat
Characterizing benthic macroinvertebrate and algal biological condition gradient models for California wadeable Streams, USA
The Biological Condition Gradient (BCG) is a conceptual model that describes changes in aquatic communities under increasing levels of anthropogenic stress. The BCG helps decision-makers connect narrative water quality goals (e.g., maintenance of natural structure and function) to quantitative measures of ecological condition by linking index thresholds based on statistical distributions (e.g., pe
Science and Products
- Science
Aquatic Ecology Group
The California Water Science Center's Aquatic Ecology Group is making great strides in research and reporting.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).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...Development of Numeric Flow Criteria to Support Freshwater Biological Objectives and Hydrologic Modification Management in California's Wadeable Streams
The State Water Resources Control Board (SWRCB) of California has initiated a process to develop numerical biological objectives for wadeable freshwater streams and rivers for the entire state. Use of biological endpoints for regulatory or compliance purposes requires the ability to relate specific stressors to key biological metrics and to use this understanding to influence management actions...Whiskeytown Aquatic Inventory Assessment
The project focuses on the assessment of aquatic biology, habitat, and water quality conditions of the major WHIS watershedsEstimating Natural Flows for Hydrologic Reference Streams
Scientists develop metrics of expected hydrological conditions at ungaged sites throughout CalliforniaApplication of the SmeltCam to Describe Processes Influencing Delta Smelt Distribution and Movements
The California Water Science Center's "SmeltCam" helps describe processes influencing Delta Smelt distribution and movement.Native Fish Population and Habitat Study - Santa Ana River
California Water Science Center scientists further research on two native fish species.Exploring Drivers of Pelagic Fish Population Decline in Bay-Delta
USGS scientists develop spatially explicit ecosystem model to explore changes pelagic fish species population and distribution in the Sacramento-San Joaquin Delta and Suisun Bay.Ecology of Selected Tidal Wetlands of the San Francisco Estuary
Researachers study differences of tidal marsh restoration efforts throughout Bay-Delta ecosystem. - Data
Santa Ana River Native Fish Population and Habitat Data, Santa Ana River, California, 2020
This dataset includes 2020 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.Data used in projected flow analysis in Yolo Bypass under 20 scenarios of climate change
Yolo Bypass is an ecological feature of the Bay-Delta ecosystem in California that provides floodplain habitat for spawning and rearing of Sacramento Splittail (Pogonichthys macrolepidotus) and rearing of juvenile Chinook Salmon (Oncorhynchus tshawytscha) when inundated. We used outputs from 10 climate change models for two Representative Concentration Pathways (RCPs) for greenhouse gas concentratSAR 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.SAR 2019 Native Fish Population and Habitat Study, Santa Ana River, California
This dataset includes 2019 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.SAR 2017 Native Fish Population and Habitat Study, Santa Ana River, California
This dataset includes: 1) microhabitat use data for fish 100 mm and larger; 2) reach fish data; and 3) reach habitat data for the Santa Ana Sucker (Catostomus santaanae) and the Arroyo Chub (Gila orcutti) in the Santa Ana River, California. Habitat availability data was not collected in 2017.SAR 2016 Native Fish Population and Habitat Study, Santa Ana River, California
Data included in this dataset include: 1) population estimate data; 2) microhabitat use data; and 3) microhabitat availability data for the Santa Ana Sucker (Catostomus santaanae) and the Arroyo Chub (Gila orcutti) in the Santa Ana River, California. - Publications
Filter Total Items: 115
Hydrodynamics 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 terChapter 1: General conceptual model for climate change in the Upper San Francisco Estuary
This report is a collaboration by many state and federal agencies working in the Upper San Francisco Estuary to analyze the potential impacts of climate change to different ecosystems found here. Management stategies for ecological values in the face of climate change require reliable and focused information. In this technical report, our focus is on the Upper San Francisco Estuary (SFE), which coFloodplains and climate change
Floodplains are landscape features that are periodically inundated by water from adjacent rivers (Opperman et al. 2010). Ecologically, functional floodplains are characterized by three primary elements: connectivity, flow regime, and spatial scale. Water quantity flowing over floodplains can vary greatly. Based on a flood’s effects on the floodplain, three flood categories have been defined: floodWarming in the upper San Francisco Estuary: Patterns of water temperature change from five decades of data
Temperature is a key controlling variable from subcellular to ecosystem scales. Thus, climatic warming is expected to have broad impacts, especially in economically and ecologically valuable systems such as estuaries. The heavily managed upper San Francisco Estuary supplies water to millions of people and is home to fish species of high conservation, commercial, and recreational interest. DespiteClimate change and fishes in estuaries
This chapter provides an overview of the main drivers of change in estuarine systems, their expected causes and impacts on estuarine fish and fisheries. An analysis of global, regional and local patterns of estuarine fish and how climate-induced change may impact estuarine systems and their fish communities is provided. We also examine the main environmental, climatic and biological stressors likeJoint-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 snorkSynthesis 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 StaDisentangling 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 elucidToward 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 recomResistance and resilience of pelagic and littoral fishes to drought in the San Francisco Estuary
Many estuarine ecosystems and the fish communities that inhabit them have undergone substantial changes in the past several decades, largely due to multiple interacting stressors that are often of anthropogenic origin. Few are more impactful than droughts, which are predicted to increase in both frequency and severity with climate change. In this study, we examined over five decades of fish monitoHydrodynamics drive pelagic communities and food web structure in a tidal environment
Hydrodynamic processes can lead to the accumulation and/or dispersal of water column constituents, including sediment, phytoplankton, and particulate detritus. Using a combination of field observations and stable isotope tracing tools, we identified how hydrodynamic processes influenced physical habitat, pelagic communities, and food web structure in a freshwater tidal system. The pelagic habitatCharacterizing benthic macroinvertebrate and algal biological condition gradient models for California wadeable Streams, USA
The Biological Condition Gradient (BCG) is a conceptual model that describes changes in aquatic communities under increasing levels of anthropogenic stress. The BCG helps decision-makers connect narrative water quality goals (e.g., maintenance of natural structure and function) to quantitative measures of ecological condition by linking index thresholds based on statistical distributions (e.g., pe
*Disclaimer: Listing outside positions with professional scientific organizations on this Staff Profile are for informational purposes only and do not constitute an endorsement of those professional scientific organizations or their activities by the USGS, Department of the Interior, or U.S. Government