Search USGS⌕ Search

SEARCH · Search USGS

Results for “Ecology of Freshwater Fish”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

1,229 records · Page 2Linked to original sources
USGS2026

Recent scientific contributions by the U.S. Geological Survey in the San Francisco Bay and Sacramento–San Joaquin Delta Estuary

Introduction The San Francisco Bay and Sacramento–San Joaquin Delta Estuary (hereafter, Bay-Delta) is the largest estuary on the West Coast of the United States. The Bay-Delta covers more than 1,600 square miles and drains a watershed of more than 75,000 square miles, which is greater than 40 percent of California. The region surrounding the Bay-Delta is home to about 10 million people, and its habitats (fig. 1) support more than 800 plant and animal species. The waterways of the Bay-Delta are the central hub of California’s extensive freshwater delivery system, supplying water to more than 27 million Californians and 4 million acres of farmland in the Central Valley. The U.S. Geological Survey (USGS) is the primary science agency of the U.S. Department of the Interior, providing a broad range of Earth, water, biological, and mapping data and expertise to inform natural resource management across the country. This fact sheet focuses on research conducted by the USGS in the Bay-Delta region, mostly within the past 5 years. The fact sheet is organized across five major themes: water flow and water quality, fish and wildlife, wetland restoration, invasive species, and hazards. In each of these areas, the USGS works closely with Federal, State, and local agencies; academia; and non-governmental organizations to provide objective, evidence-based science. The data and knowledge gained from USGS research and monitoring are publicly available and are routinely used by agencies, including the U.S. Bureau of Reclamation, U.S. Army Corps of Engineers, U.S. Fish and Wildlife Service, California Department of Water Resources, California Department of Fish and Wildlife, California State Water Resources Control Board, Delta Stewardship Council, and many additional organizations and stakeholders to inform management of the Bay-Delta region and its resources.

California↗
USGS2026

Transcriptional changes in wild Yukon River Chinook Salmon associated with Ichthyophonus infections

Objective We compared differentially expressed genes in Chinook Salmon Oncorhynchus tshawytscha with three divergent Ichthyophonus statuses (undetected, subclinical infections, or clinical disease; n = 100) to investigate associated transcriptomic responses. Disease associated with the fish parasite Ichthyophonus sp. was first diagnosed in adult Chinook Salmon from the Yukon River in the late 1980s and has subsequently been implicated in premature host mortality. Methods Chinook Salmon tissue sample collections and Ichthyophonus infection data were leveraged from a multi-agency collaboration during summer 2022 at three locations along the main-stem Yukon River that spanned nearly 2,000 km of freshwater migration (lower, middle, and upper river). We sequenced the transcriptome and compared this to infection status based on routine diagnostic procedures. Results Among the 17,569 genes for which messenger RNA was detected, we identified a transcription signature in the skeletal muscle that was associated with Ichthyophonus infections and included 53 differentially expressed genes. The differentially expressed genes and their pathways included those known for involvement in immune functions, energy synthesis, cellular breakdown, and reproduction—all processes that are known to be influenced by senescence during spawning migrations. Conclusions Results demonstrate a clear transcriptional difference between diseased fish (clinical disease group) and those in which Ichthyophonus was undetected, including identifying candidate markers for infection in this population. These results provide a foundation for development of nonlethal biomarkers to evaluate potential Ichthyophonus infections in Chinook Salmon based on gene transcription, protein products, or gene variants (e.g., polymorphisms).

Journal of Aquatic Animal Health↗
USGS2026

Rewilding the upper Klamath River Basin: Rapid recolonization of Chinook salmon following the world’s largest dam removal

Habitat fragmentation is a global driver of decline in biodiversity, yet evaluations of ecological response following re-connection remain rare. In 2024, four hydroelectric dams on the Klamath River were removed, reconnecting over 640 km of anadromous habitat and marking the largest dam removal project completed to date. We used a stationary high-resolution multi-beam imaging SONAR to quantify adult Chinook salmon ( Oncorhynchus tshawytscha ) passage into newly reopened reaches during the first two migratory seasons following dam removal. An estimated 7,742 (95% CI: 7,702–7,778) Chinook salmon migrated upstream in 2024 and 13,310 (95% CI: 12,876–13,733) in 2025, representing 18–19% of fish returning to the Klamath River Basin. Within this period, Chinook salmon recolonized 88% of their documented historical distribution, expanding into 345 km of reconnected habitats and reaching elevations of up to 1,250 m. Recolonization required fish to swim through dam removal sites, complex hydraulic corridors and engineered fishways, demonstrating the propensity for rapid recolonization at basin scale despite these challenges. These findings provide the first quantitative assessment of salmon response to the world’s largest dam removal and demonstrate how reconnection can catalyze large-scale recolonization in historically fragmented river networks.

California, Oregon↗
USGS2026

Ice sheet dynamics drive pronounced changes in the subsurface freshwater-saltwater interface

Saltwater is migrating into freshwater aquifers globally with water quality and biogeochemical implications, yet saltwater intrusion in glaciated regions is sparsely investigated. Field observations suggest that groundwater head in glaciated systems is influenced by ice sheet forcings and provides evidence that seawater infiltrated into offshore aquifers during past deglaciation events. To understand links between ice sheet dynamics, groundwater head, and saltwater intrusion, we use numerical models to explore the effects of deglaciation on nearshore head and salinity distributions. We find that ice sheet thinning diminishes groundwater head, and the resulting shift in subsurface pressure gradients drives rapid landward movement of the subsurface freshwater-saltwater interface up to 4.0 km or 1.3 m per m ice sheet loss. Results highlight an overlooked saltwater intrusion mechanism that aligns with field observations and affects glaciated coastlines undergoing ice sheet retreat, underscoring the need to consider this mechanism in studies of contemporary coastal water quality.

Geophysical Research Letters↗
USGS2000

Method for estimating water use and interbasin transfers of freshwater and wastewater in an urbanized basin

Techniques for management of drainage basins that use water budgets to balance available water resources with actual or anticipated water use require accurate and precise estimates of basin withdrawals, interbasin transfers of freshwater, unaccounted-for use, water use, consumptive use, inflow and infiltration, basin return flow, and interbasin transfers of wastewater. Frequently, interbasin transfers of freshwater and wastewater are not included in basin water budgets because they occur within public water-delivery and wastewater-collection systems. A new 10-step method was developed to improve estimates of inflow and infiltration and interbasin transfers using readily available statewide data. The accuracy and precision of water-use estimates determined by this method are improved through careful application of coefficients for small users and the use of metered values for large users. The method was developed and tested with data for the Ten Mile River Basin in southeastern Massachusetts. This report uses examples from the basin to illustrate each step of the method.

Massachusetts↗
USGS2026

Assessing the state of hydrologic science in the Upper Klamath Basin—A comprehensive review of data, tools, and models

Water demand in the Upper Klamath Basin (UKB) from various stakeholders and ecological needs often outstrips available supply, leading to persistent management challenges. This study reviews the state of hydrologic science within the UKB as of 2025—specifically, the tools, data, and models available for assessing five key components of the water system: (1) surface water; (2) precipitation; (3) evapotranspiration; (4) groundwater; and (5) water use. The UKB water supply is critical for Native American communities, regional agriculture, and federally listed fishes and faces challenges from competing needs, climate variability, and operational/regulatory requirements. We assess existing datasets, regional and national models, and historical studies to understand the available resources and identify gaps that may hinder integrated water assessments and management. Our findings indicate areas where improvements in data collection and model precision could improve the accuracy of water-availability forecasts and support water-management practices. This review can inform near-term forecasting, assist in optimizing water-resource data collection and management strategies, and support regional water-availability assessments of the basin.

Oregon↗
USGS2026

Transit time modeling framework for predicting freshwater salinization in urban catchments

The salinity of inland freshwaters is rising globally, particularly in urban watersheds where winter road deicers are widely applied. Attributing stream salinity dynamics to specific sources and transport pathways remains challenging due to episodic salt inputs, engineered drainage, and strong coupling between hydrology and subsurface storage. We present a modeling framework that couples climate-driven deicer build-up and wash-off with transient transit time distribution theory to simulate salt transport through drainage, interflow, and groundwater pathways. Applied to an urban watershed in Northern Virginia (USA), the model reproduces ten years of high-frequency stream salinity measurements across daily-to-decadal timescales. The calibrated model implies an average deicer application of 206 tonnes Cl −1 yr −1 , or roughly one 20 kg bag of rock salt person −1 yr −1 when normalized by the 20,000 people living in the watershed. In winter months, higher infiltration routes a large fraction of snowmelt and deicers into shallow subsurface pathways, enhancing vadose-zone and interflow contributions to stream salinity. Limited subsurface storage capacity and seasonal hydrologic turnover flush excess chloride from the vadose zone and groundwater during subsequent summer storms. By linking climate-driven deicer inputs, hydrologic connectivity, and stream water age, the framework provides a transferable basis for diagnosing and managing freshwater salinization in urban watersheds.

Virginia↗
USGS2025

Dietary bioavailability of uranium to a model freshwater invertebrate

Uranium (U) mining increases environmental exposures. Understanding how U is taken up by organisms can aid in evaluating the potential for bioaccumulation and toxicity. Although the importance of aqueous geochemical speciation is well recognized for U bioavailability after dissolved exposures, far less is known about the processes controlling U bioavailability after dietary exposures. This study characterizes the biogeochemical drivers of dietary U uptake in the freshwater snail Lymnaea stagnalis in laboratory experiments. Solids tested included benthic diatoms pre-exposed to dissolved U(VI), soils from contaminated U mine sites, and colloidal hydrous ferric oxide (HFO) synthesized in the presence of dissolved U(VI) or with U complexed by natural organic matter (NOM). Results showed that U was bioavailable from all solids. Uranium assimilation efficiency (AE), a proxy for dietary U bioavailability, varied among solids. AE was lowest for the U-contaminated soils (25 ± 17%) and highest for the U-laden diatoms (71 ± 13%). AE varied slightly among HFO preparations, suggesting modest influences of NOM and iron on U bioavailability. Increases in dietary U exposures reduced feeding rates, and the extent of feeding inhibition appeared inversely related to U bioavailability. The high U assimilation and range of bioavailability have implications for toxicity risks inferred without considering dietary uptake.

Environmental Science and Technology↗
USGS2026

Spatially referenced watershed models for the binational Red–Assiniboine River Basin: Bayesian vs frequentist comparison

Excess nutrient loading remains a leading cause of declining water quality in lakes, estuaries, and coastal waters worldwide, with global economic costs of US$200 billion – US$2 trillion annually from impacts on fisheries, tourism, freshwater resources, and water treatment. Our study focuses on total phosphorus (TP) in Lake Winnipeg and its binational Red-Assiniboine River Basin, where nutrient inputs have degraded water quality and increased cyanobacterial blooms. These changes pose ecological, public health, and economic risks. We applied a spatially referenced watershed model with a hybrid statistical-mechanistic structure partitioning annual nutrient loads into land-use export, land-to-water delivery, and in-reservoir decay. Bayesian and traditional frequentist model calibrations were compared. In the frequentist model, coefficients for agricultural inputs, forests /wetlands, stream channels, precipitation, and reservoir losses were statistically significant, whereas coefficient for wastewater was not. In contrast, all variables were successfully calibrated using the Bayesian approach. Model results delineate TP-export hotspots across the basin, showing that 54–62% of TP originates from the U.S., with agricultural sources ranging 62–72%—highlighting the importance of agriculture-focused Best Management Practices. Given the global relevance of nutrient-driven water-quality challenges, our results highlight Bayesian calibration for robust risk assessment and adaptive nutrient management.

Red–Assiniboine River Basin↗
USGS2026

A geographic dataset of rocky reefs habitat areas of particular concern for the United States West Coast

The United States National Marine Fisheries Service determines “essential fish habitat (EFH)” for federally managed species in coordination with regional fishery management councils, considers adverse effects to those habitats, and provides information to further habitat conservation and enhancement. Identifying discrete subsets of EFH as “habitat areas of particular concern (HAPC)” can help focus conservation, management, and research efforts. In 2006, the Pacific Fishery Management Council designated rocky reefs along the United States (U.S.) West Coast as HAPCs for groundfishes because of their ecological significance, sensitivity to human impacts, and relative rarity. To better understand where rocky reefs occur, we (1) located rocky reef areas that were not included in the 2006 rocky reef dataset, and (2) incorporated best available data into a refined geographic dataset that enables visualization. Our update shows that rocky reefs are distributed throughout the U.S. West Coast continental margin, are patchier than previously known, and comprise 8% of the extent of all data inputs. This updated dataset will inform resource management decisions in coastal and marine environments.

California, Oregon, Washington↗
USGS2024

Joint pilot fish habitat framework

This story map will take you through the process of exploring and testing methods necessary for a higher resolution, seamless fish habitat assessment across both inland and estuarine waters through the lens of our joint pilot assessment Fish habitat assessments attempt to relate past, current, or future landscape conditions to the state of fish species occurrence, distribution, abundance, or community and habitat condition in streams, rivers, or estuaries. Previous fish habitat assessments, such as the National Fish Habitat Assessment, conducted separate and disconnected assessments for inland waters and estuaries. In this project, National Oceanic and Atmospheric Administration ( NOAA ) and U.S. Geological Survey ( USGS ) researchers created a seamless spatial framework to allow assessments that integrate influences on fish habitat from headwaters to the estuary. This effort began when the Chesapeake Bay Program Fish Habitat Action Team expressed interest in a Baywide fish habitat assessment spanning tidal salt, tidal fresh, warm non-tidal, and cold non-tidal waters. However, the complexity of the myriad of implementation details to consider when developing such an assessment necessitated the need for a tributary-specific pilot assessment. To conduct this pilot assessment, a NOAA/USGS joint partnership was formed with cooperation and support from the Chesapeake Bay Agreement and Chesapeake Bay Fish Habitat Action Team (FHAT).

Maryland↗
USGS2026

Identifying overlap between native fish movements and a possible seasonal Grass Carp deterrent in the Sandusky River, Ohio, USA

Riverine fishes are vulnerable to habitat fragmentation caused by interrupted access to vital habitats. Fragmentation using artificial structures can be used to limit the spread of invasive fishes by inhibiting movement between critical habitats. Thus, tradeoffs exist between maintaining connectivity for native species and restricting movement of invasive fishes. A nonphysical deterrent has been proposed to prevent invasive Grass Carp ( Ctenopharyngodon idella ) from reaching spawning habitats in the Sandusky River, a tributary to Lake Erie, during late spring–summer. However, this timing overlaps with spawning periods of a suite of native fishes. We used acoustic telemetry and ichthyoplankton surveys to examine movement and spawning activity of multiple native species and to assess potential impacts of deterrent operation on reproduction. All species used the proposed deterrent location during the Grass Carp spawning period, and their movements corresponded with larval fish collections, indicating upstream spawning. These findings suggest the deterrent could unintentionally restrict native species’ access to essential habitats. Balancing habitat connectivity and invasive species control will likely depend on species-specific responses and careful timing of deterrent operation.

Ohio↗
USGS1998

Trace elements in streambed sediment and fish liver at selected sites in the Upper Colorado River Basin, Colorado 1995-96

Trace elements were analyzed in streambed-sediment samples collected from 16 sites and in fish-liver samples collected from 14 sites in the Upper Colorado River Basin in Colorado as part of the National Water-Quality Assessment program. Sites sampled represented agricultural, mining, mixed, and urban/recreation land uses and background conditions. The results for 15 trace elements in streambed-sediment and in fish-liver samples are presented in this report. Fourteen of the selected trace elements were detected in streambed-sediment samples collected at all sites. Twelve of the selected trace elements were detected in fish liver at more than 50 percent of the sites. Cadmium, copper, selenium, and zinc were selected for a more detailed analysis. Cadmium, copper, and zinc concentrations in streambed sediment were highest at mining land-use sites in the Southern Rocky Mountains physiographic province. Selenium concentrations in streambed sediment were highest at an agricultural land-use site in the Colorado Plateau physiographic province. The concentration of trace elements in streambed sediment generally increased as particle size decreased. Concentrations of trace elements in fish liver generally did not follow the same relation to land use as concentrations in streambed sediment; however, cadmium concentrations in fish liver were highest at a mining land-use site in the Southern Rocky Mountains physiographic province, and selenium concentrations in fish liver were highest at an agricultural land-use site in the Colorado Plateau physiographic province. Copper and zinc concentrations in fish liver were highest at mixed land-use sites. Comparison of streambed-sediment and fish-liver concentrations to two other similar NAWQA studies in the Rocky Mountain region generally indicated similar patterns in relation to land use for streambed sediment, but not for fish liver. Cadmium, copper, and zinc concentrations in streambed sediment were highest at sites affected by mining in all three study units. Selenium concentrations in streambed sediment did not indicate relations among the three study units when compared to land use. Cadmium in fish liver was highest at sites affected by mining in all three study units. Copper, selenium, and zinc in fish liver did not indicate relations among the three study units when compared to land use.

Colorado↗
USGS2025

Linking permafrost to the abundance, biomass, and energy density of fish in Arctic headwater streams

Permafrost thaw alters groundwater flow, river hydrology, stream-catchment interactions, and the availability of carbon and nutrients in headwater streams. The impact of permafrost on watershed hydrology and biogeochemistry of headwater streams has been demonstrated, but there is little understanding of how permafrost influences fish in these ecosystems. We examined relations among permafrost characteristics, the resulting changes in water temperature, stream hydrology (e.g., discharge flashiness), and macroinvertebrates, with the abundance, biomass, and energy density of juvenile Dolly Varden ( Salvelinus malma ) and Arctic Grayling ( Thymallus arcticus ) across 10 headwater streams in northwestern Alaska. Macroinvertebrate density was driven by concentrations of dissolved carbon and nutrients supporting stream food webs. Dolly Varden abundance was primarily related to water temperature with fewer fish in warmer streams, whereas Dolly Varden energy density decreased with the flashiness of the headwater streams. Dolly Varden biomass was related to both temperature and bottom-up food web effects. The energy density of Arctic Grayling decreased with warmer temperatures and discharge flashiness. These relations demonstrate the importance of terrestrial–aquatic connections in permafrost landscapes and indicate the complexity of landscape effects on fish. Because permafrost thaw is one of the most impactful changes occurring as the Arctic warms, an improved understanding of how stream temperature, hydrology, and bottom-up food web processes influence fish populations can aid forecasting of future conditions across the Arctic.

Alaska↗
USGS2026

A targeted approach for mapping groundwater discharge to surface water and fish thermal refuge in four Lake Ontario tributaries

The duration, magnitude, and frequency of heatwaves are predicted to increase in the coming decades, a combination that can reduce the survival of many fish species. Across the world, there is broad interest in identifying thermal refuge for heat-intolerant fish species and exploring opportunities to enhance or protect these areas. Because deeper groundwater maintains a relatively constant temperature, groundwater-influenced areas along streams can provide cool-water refuge for fish during periods of extreme heat. A targeted approach was developed for identifying existing cold-water zones and areas of substantial groundwater discharge in four high priority Lake Ontario tributaries. Our approach included: (1) predicting where groundwater discharge is most likely with a simple geospatial model and (2) using model predictions to select field sites for intensive high-resolution study, including ground-based mapping of groundwater features (springs, seeps, tributaries) as well as drone-based optical and thermal infrared surveys. Results from field sites were used to both verify model performance and map different types and aerial extents of thermal anomalies. Geospatial modelling successfully predicted regions of widespread groundwater upwelling, later verified and mapped by field and drone surveys. Comparison of model and field survey results further highlighted specific geospatial layers, such as soil/bedrock types and topographic wetness index, as being particularly useful for predicting groundwater influence on streams in the study area. In addition, a comparison of geospatial model results with a model of fish abundances along the studied streams showed significant positive correlations for many heat-intolerant fish species over a wide geographic area. The approach developed in this study can be applied to other watersheds to highlight areas of probable groundwater discharge and could be used by fishery and water resource managers to support cold-water fish habitat management decision-making and resource conservation.

New York↗
USGS2026

Tectonically driven integration of the 4.8 Ma Colorado River USA tracked with detrital sanidine and fish genetics

The development of the continental-scale Colorado River system, western USA, from 8 to 4.8 Ma, is revealed using 60-40 Ma detrital sanidine tracer grains and fish phylogeny. Here we show that precursor paleoriver segments became integrated north to south as traced by 60-40 Ma sand grains that were derived from the north and sequentially appeared in the 25-8 Ma Browns Park Formation of Utah, 7-6 Ma upper Bidahochi Formation of Arizona, and 4.8 Ma Bouse Formation of the lower Colorado River and proto Gulf of California. This timing is mimicked by molecular clock estimates of divergence times among fish lineages. River integration was a response to headwater uplifts in the Yellowstone hotspot track and Rocky Mountains. 40 Ar/ 39 Ar ages refine the timing for mantle-drips that caused subsidence, then uplift, of depositional basins that influenced the integration pathway and tempo. The ~ 3-million-year timescale suggests that multiscale mantle-driven uplift, rather than lake spillover, was the primary driver for integration of the proto-Colorado River through Grand Canyon.

Colorado River↗
USGS2026

Effects of a low-lipid diet on the gut microbiome and head kidney transcriptome of juvenile Chinook Salmon

Objective Pacific salmon Oncorhynchus spp. reared in production hatcheries are typically fed high-lipid, energy-dense diets to achieve large size and high body condition prior to release. In contrast, juveniles in natural environments tend to consume low-lipid, high-protein diets, and fish reared for research or conservation purposes are sometimes fed diets that are formulated to mimic natural diets and promote wild-like phenotypes. Understanding how these alternative diets affect fish health beyond growth and body condition could ultimately contribute to improving hatchery fish fitness. Methods In this work, we evaluated changes in the fecal microbiome and gene expression of juvenile Chinook Salmon O. tshawytscha on a standard high-lipid hatchery diet versus a low-lipid diet formulated to mimic the nutrition profile of natural-origin fish. To evaluate the time scale at which diet alters the fecal microbiome, we collected longitudinal samples over a 12-week period and switched the diets of a subset of fish twice during the experiment. We used 16S ribosomal RNA gene amplicon sequencing to characterize fecal microbiome differences between fish on the two diets as well as hatchery-reared fish at a production hatchery, hatchery fish that had been captured after release into a stream, and natural-origin, stream-reared fish of similar ages. Additionally, we conducted RNA sequencing on head kidney samples from laboratory-reared fish to evaluate changes in gene expression in this important immune organ. Results We found that the low-lipid diet and the hatchery diet resulted in microbiomes that differed from the microbiome of natural-origin fish and from each other and that diet-driven changes to the microbiome could occur in under 14 d. The low-lipid diet did not result in a microbiome that resembled the microbiome of naturally produced fish. Instead, the low-lipid diet resulted in a microbiome community that was distinct from those of fish reared on the hatchery diet and fish sampled from the wild. The RNA sequencing results indicated differential enrichment of pathways related to immunity, metabolism, and hormone synthesis between fish that were fed the two experimental diets. Conclusions The results suggest that additional environmental factors influence the microbiome more strongly than diet formulation or that the low-lipid diet has a smaller effect on the microbiome than a natural, ­invertebrate-based diet. Given that the gut microbiome and systemic immune function contribute significantly to disease resistance, our findings highlight the importance of understanding how diets fed to fish in captivity may affect fish health beyond growth and body condition metrics.

Journal of Aquatic Animal Health↗