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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↗

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

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↗

USGS2026

Using a temporary emigration model to estimate abundance of stream fishes from hybrid removal surveys with and without block nets

Monitoring programs are often faced with a decision to allocate resources into either robust spatiotemporal coverage to estimate a population index (e.g., not true abundance) or confirming closed sampling conditions (e.g., with block nets) for an unbiased population estimate at the cost of spatiotemporal coverage. However, making accurate and precise abundance estimates at robust spatiotemporal scales is possible when combining open and closed sampling designs with integrated modeling techniques. We used simulations and a case study of backpack electrofishing surveys in the Santa Ana River, California to test the efficacy of an integrated abundance model (temporary emigration model, TE) to estimate abundance of fishes using removal sampling methods with a hybrid sampling design (sampling with and without block nets during removal sampling). We found that the TE model performed well under most modeling scenarios (sample size, amount of closure violation, number of samples collected during closure), although at least a few samples with block nets were necessary for all parameters to be estimable. When applied to fish surveys in the Santa Ana River, we found that catch of the fishes fit to the TE model (Santa Ana Sucker, Arroyo Chub, Channel Catfish, Largemouth Bass, Yellow Bullhead) showed little evidence that the closure assumption was violated when block nets were not used. Additionally, we found that the abundance of non-native fishes negatively affected the abundance of the native Santa Ana Sucker, which was also found to adversely affect the native fish’s access to critical habitat consisting of gravel and cobble substrate. Our results indicate that the TE model presents a viable solution to common sampling problems that impact many monitoring programs, where precise and accurate population estimates can be made at large spatiotemporal scales even when most samples violate the closure assumption.

California↗

USGS2024

Aboveground carbon stocks across a hydrological gradient: Ghost forests to non-tidal freshwater forested wetlands

Upper estuarine forested wetlands (UEFWs) play an important role in the sequestration of atmospheric carbon (C), which is facilitated by their position at the boundary of terrestrial and maritime environments but threatened by sea level rise. This study assessed the change in aboveground C stocks along the estuarine–riverine hydrogeomorphic gradient spanning salt-impacted freshwater tidal forested wetlands to freshwater forested wetlands in seasonally tidal and nontidal landscape positions. Standing stocks of C in forested wetlands were measured along two major coastal river systems, the Winyah Bay in South Carolina and the Savannah River in Georgia (USA), replicating and expanding a previous study to allow the assessment of change over time. Aboveground C stocks on these systems averaged 172.9 Mg C ha −1 , comparable to those found in UEFWs across the globe and distinct from the terrestrial forested ecosystems they are often considered to be a part of during large-scale C inventory efforts. Groundwater salinity conditions as low as 1.3 ppt were observed in conjunction with losses of aboveground C. When viewed in context alongside expected sea level rise and corresponding saltwater intrusion estimates, these data suggest a marked decrease in aboveground C stocks in forested wetlands situated in and around tidal estuaries.

Georgia, South Carolina↗

USGS2025

‘The fish that stop’: Drivers of historical decline for Pacific cod and implications for modern management in an era of rapidly changing climate

n the Gulf of Alaska, a series of marine heat waves depleted Pacific cod ( Gadus macrocephalus ) biomass to the lowest abundance ever recorded and led to the fishery’s closure in 2020. Although the fishery has been productive for decades, this collapse may have historical precedents. Traditional knowledge holders refer to cod as ‘the fish that stop’, and there is a suggested period of decline in the 1930s. Here we conduct a catch reconstruction of the early commercial fishery (1864–1950), confirming a rapid catch decline in the 1920s and 1930s. Next, we evaluate evidence for possible drivers. We document changes to demand and technology that contributed to declining catch. However, we also find both qualitative and quantitative evidence of depletion, suggesting catch declines were not driven entirely by social factors. Overfishing may have contributed to localized catch declines as evidenced by declining catch rates in heavily fished localities. We also find evidence for climate as a driver of regional decline, with the period of catch decline characterized by up to 2°C higher temperatures as compared to the earlier period of high fisheries production. Our analysis underscores the importance of understanding long-term drivers of fisheries productivity and the value of linking fisheries and climate histories.

Alaska↗

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↗

USGS2024

Projected sea-level rise and high tide flooding at Timucuan Ecological and Historic Preserve, Florida

Introduction National parks and preserves in the South Atlantic-Gulf Region contain valuable coastal habitats such as tidal wetlands and mangrove forests, as well as irreplaceable historic buildings and archeological sites located in low-lying areas. These natural and cultural resources are vulnerable to accelerated sea-level rise and escalating high tide flooding events. Through a Natural Resources Preservation Program-funded project during 2021–23, the U.S. Geological Survey, in collaboration with the National Park Service, estimated the probability of inundation at Timucuan Ecological and Historic Preserve, Florida, and several other parks under various sea-level rise scenarios and contemporary high tide flooding thresholds. The maps produced for this effort can be used to assess potential habitat change and explore how infrastructure and cultural resources within the park may be exposed to future flooding-related hazards.

Florida↗

USGS2024

Factors contributing to pesticide contamination in riverine systems: The role of wastewater and landscape sources

Wastewater treatment plant (WWTP) discharges can be a source of organic contaminants, including pesticides, to rivers. An integrated model was developed for the Potomac River watershed (PRW) to determine the amount of accumulated wastewater percentage of streamflow (ACCWW) and calculate predicted environmental concentrations (PECs) for 14 pesticides in non-tidal National Hydrography Dataset Plus Version 2.1 stream segments. Predicted environmental concentrations were compared to measured environmental concentrations (MECs) from 32 stream sites that represented a range of ACCWW and land use to evaluate model performance and to assess possible non-WWTP loading sources. Statistical agreement between PECs and MECs was strongest for insecticides, followed by fungicides and herbicides. Principal component analysis utilizing optical fluorescence and ancillary water quality data identified wastewater and urban runoff sources. Pesticides that indicated relatively larger sources from WWTPs included dinotefuran, fipronil, carbendazim, thiabendazole, and prometon whereas imidacloprid, azoxystrobin, propiconazole, tebuconazole, and diuron were more related to urban runoff. In addition, PECs generally comprised a low proportion of MECs, which indicates possible dominant loading sources beyond WWTP discharges. Cumulative potential toxicity was higher for sites with greater ACCWW and/or located in developed areas. Imidacloprid, fipronil, and carbendazim accounted for the largest portion of predicted potential toxicity across sites. The chronic aquatic life toxicity benchmarks for freshwater invertebrates were exceeded for 82 % of the imidacloprid detections ( n = 28) and 47 % of the fipronil detections ( n = 19). These results highlight the ecological implications of pesticide contamination from WWTP discharges and also the potential legacy effects from accumulated soil and groundwater sources. Pesticide management strategies that mitigate both current and historical impacts may improve the health of aquatic ecosystems.

Potomac River watershed↗

USGS2024

Characterization of the water resources of the Pamunkey River watershed in Virginia—A review of water science, management, and traditional ecological knowledge

In central Virginia, the Pamunkey Indian Tribe and Reservation are facing increasingly complex water resource issues related to quantity and quality. Documentation of surface-water, groundwater, water quality, land subsidence, sea-level rise, and river ecology issues in the Pamunkey River watershed and incorporation of traditional ecological knowledge into these research topics may improve understanding of the water resources broadly. This report summarizes the relevant traditional ecological knowledge and scientific literature to elucidate gaps in the total combined knowledge of a suite of water science topics concerning the Pamunkey River watershed. This suite of water science topics includes some of the issues that the Pamunkey Indian Tribe and Reservation are facing within the watershed: fragmentation of streams and management of streamflow, flooding, degrading water quality, groundwater extraction, relative sea-level rise, rapid changes in ecosystems, loss of ecological and biological diversity, and climate change. Gaps in total combined knowledge are pervasive throughout each of these water resource topics. Identifying these knowledge gaps can help inform future research and management strategies.

Virginia↗

USGS2026

Navigating uncertainty and competing objectives: Spring chinook salmon recovery in the upper Willamette river

Globally, anadromous fish populations are threatened with extinction due to multiple factors, including river impoundments that block migration, widespread alteration of physical habitat, temperature, and flow regimes, commercial and recreational harvest, changes in biological communities, and long-term climate trends. In this synthesis, we describe how physical and biological factors, policy and law, and public resource allocation affect management of spring-run Chinook Salmon ( Oncorhynchus tshawytscha ) in the Upper Willamette River (UWR), Oregon, USA. Efforts to restore salmon populations often involve trade-offs, for example, water management decisions must account for flood control, agricultural and municipal water use, and management of other species. UWR Chinook Salmon recovery efforts are also governed by multiple laws, policies, and action agencies that in some cases have incongruent objectives. Competing and conflicting objectives, combined with uncertainty regarding the outcomes of proposed management actions, create significant challenges for decision makers. Resource limitations, regulatory constraints, and incongruent objectives have created challenges for managers in the UWR, but opportunities exist for improved adaptive management and collaboration, which could build trust and engagement among stakeholders and ultimately support the successful implementation of decision tools. A suite of decision support tools that have been used in the Willamette River basin and elsewhere across the range of Pacific salmon have the potential to enhance decision processes. These tools can be effective when decision makers and stakeholders commit to long-term, collaborative utilization of the tools for decision making, and when available resources and regulatory environments are conducive to implementation and adaptive refinement of both the decision-support tools and management plans. The general biological and institutional principles discussed for UWR Chinook Salmon in this work apply more generally to populations of anadromous fishes across their range, especially to populations in highly regulated river systems.

Oregon↗

USGS2025

Integrating marine historical ecology into management of Alaska’s Pacific cod fishery for climate readiness

The Pacific cod ( Gadus macrocephalus ) fishery was closed in 2020 after a rapid decline in biomass caused by the marine heat waves of 2014–2019. Pacific cod are exceptionally thermally sensitive and management of this fishery is now challenged by increasingly unpredictable climate conditions. Fisheries monitoring is critical for climate readiness, but short-term monitoring data may be inadequate for recognizing and anticipating change under rapid climate changes. We propose an interdisciplinary, marine historical ecology framework that looks to long-term records (local and traditional knowledge, history, archaeology, and paleoclimatology) to capture a long range of ecological variability and provide historical context for management. In order to connect to contemporary fisheries management, this framework must be built on a common vocabulary and an understanding of the key metrics used in fisheries stock assessments. Here, we propose metrics derived from Pacific cod stock assessment and synthesize information relevant to understanding the effects of past warming periods on cod populations across the Gulf of Alaska and Bering Sea. This case study provides a framework for thinking about how to use these historical records in the context of fisheries management under rapidly changing climate conditions.

Alaska↗

USGS2024

Biogeochemical and community ecology responses to the wetting of non-perennial streams

Transitions between dry and wet hydrologic states are the defining characteristic of non-perennial rivers and streams, which constitute the majority of the global river network. Although past work has focused on stream drying characteristics, there has been less focus on how hydrology, ecology and biogeochemistry respond and interact during stream wetting. Wetting mechanisms are highly variable and can range from dramatic floods and debris flows to gradual saturation by upwelling groundwater. This variation in wetting affects ecological and biogeochemical functions, including nutrient processing, sediment transport and the assembly of biotic communities. Here we synthesize evidence describing the hydrological mechanisms underpinning different types of wetting regimes, the associated biogeochemical and organismal responses, and the potential scientific and management implications for downstream ecosystems. This combined multidisciplinary understanding of wetting dynamics in non-perennial streams will be key to predicting and managing for the effects of climate change on non-perennial ecosystems.

Nature Water↗

USGS2025

Microbial ecology of permafrost soils: Populations, processes, and perspectives

Permafrost microbial research has flourished in the past decades, due in part to improvements in sampling and molecular techniques, but also the increased focus on the permafrost greenhouse gas feedback to climate change and other ecological processes in high latitude and alpine permafrost soils. Permafrost microorganisms are adapted to these extreme environments and remain active at low temperatures and when resources are limited. They are also an important component of global elemental cycles as they regulate organic matter turnover and greenhouse gas production, particularly as permafrost thaws. Here we review the permafrost microbiology literature coupled with an exploration of its historical aspects, with a particular focus on a new understanding advanced by molecular biology techniques. We further identify knowledge gaps and ways forward to improve our understanding of microbial contributions to ecosystem biogeochemistry of permafrost-affected systems.

Permafrost and Periglacial Processes↗

USGS2024

Complex hydrology and variability of nitrogen sources in a karst watershed

Streams draining karst areas with rapid groundwater transit times may respond relatively quickly to nitrogen reduction strategies, but the complex hydrologic network of interconnected sinkholes and springs is challenging for determining the placement and effectiveness of management practices. This study aims to inform nitrogen reduction strategies in a representative agricultural karst setting of the Chesapeake Bay watershed (Fishing Creek watershed, Pennsylvania) with known elevated nitrate contamination and a previous documented groundwater residence time of less than a decade. During baseflow conditions, streamflow did not increase with drainage area. Headwaters and the main stem lost substantial flow to sinkholes until eventually discharging along large springs downstream. Seasonal hydrologic conditions shift the flow and nitrogen load spatially among losing and gaining stream sections. A compilation of nitrogen source inputs with the geochemistry and the pattern of enrichment of δ 15 N and δ 18 O suggest that the nitrogen in streams and springs during baseflow represents a mixture of manure, fertilizer, and wastewater sources with low potential for denitrification. The pH and calcite saturation index increased along generalized flow paths from headwaters to springs and indicate shorter groundwater residence times in baseflow during the spring versus summer. Given the substantial investment in management practices, fixed monitoring sites could incorporate synoptic water sampling to properly monitor long-term progress and help inform management actions in karst watersheds. Although karst watersheds have the potential to respond to nitrogen reduction strategies due to shorter groundwater residence times, high nitrogen inputs, effectiveness of conservation practices, and release of legacy nutrients within the karst cavities could confound progress of water quality goals.

Pennsylvania↗