Search USGS⌕ Search

SEARCH · Search USGS

Results for “Aquatic Ecology”

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.

At least 811 records · Page 45Linked to original sources
USGS2020

Trends and biological effects of environmental contaminants in lamprey

Environmental contamination is of global concern. Lamprey are scientifically, ecologically, culturally, and economically important fishes. Our study represents the first synthesis ever on environmental contamination in lamprey. Objectives of this study include: (1) evaluate lethal and sublethal effects of environmental contaminants on lamprey, thereby providing insight into the potential for environmental contaminants to affect lamprey abundance, (2) highlight the unique characteristics of contaminant accumulation in lamprey, (3) determine whether spatial and temporal trends observed in contaminant concentrations of other top predators of aquatic food webs are reflected in the spatial and temporal trends of contaminant concentrations of lamprey, (4) identify key environmental contaminants affecting consumption advisories for people eating lamprey, and (5) identify important gaps in our knowledge of environmental contamination in lamprey. The geographic scope of this synthesis is worldwide. We conclude that, in general, the environmental contaminant concentrations that have been experienced by lamprey in the wild appear to be nonlethal to lamprey. However, environmental contaminants exert sublethal effects on lamprey. Sea lamprey ( Petromyzon marinus ) and Pacific lamprey ( Entosphenus tridentatus ) are relatively high in total mercury (Hg) concentration compared with other fishes. Compared with other top predators, lamprey are relatively low in polychlorinated biphenyl (PCB) concentration and concentrations of organochlorine pesticides. We also conclude that regulations on the use of PCBs, beginning in the 1970s, were effective in dramatically reducing PCB concentration in lamprey since the 1970s. Emerging contaminants, such as pharmaceuticals, microplastics, and per- and polyfluorinated alkyl substances (PFAS), have yet to be studied in lamprey.

Journal of Great Lakes Research↗
USGS2011

Approach for environmental baseline water sampling

Samples collected during the exploration phase of mining represent baseline conditions at the site. As such, they can be very important in forecasting potential environmental impacts should mining proceed, and can become measurements against which future changes are compared. Constituents in stream water draining mined and mineralized areas tend to be geochemically, spatially, and temporally variable, which presents challenges in collecting both exploration and baseline water-quality samples. Because short-term (daily) variations can complicate long-term trends, it is important to consider recent findings concerning geochemical variability of stream-water constituents at short-term timescales in designing sampling plans. Also, adequate water-quality information is key to forecasting potential ecological impacts from mining. Therefore, it is useful to collect baseline water samples adequate tor geochemical and toxicological modeling. This requires complete chemical analyses of dissolved constituents that include major and minor chemical elements as well as physicochemical properties (including pH, specific conductance, dissolved oxygen) and dissolved organic carbon. Applying chemical-equilibrium and appropriate toxicological models to water-quality information leads to an understanding of the speciation, transport, sequestration, bioavailability, and aquatic toxicity of potential contaminants. Insights gained from geochemical and toxicological modeling of water-quality data can be used to design appropriate mitigation and for economic planning for future mining activities.

Conference Paper↗
USGS2021

Fragmentation and streamflow metrics drive prairie chub (Macrhybopsis australis) occurrence in the upper Red River basin

Dam construction threatens global aquatic biodiversity by fragmenting stream networks and altering flow regimes. The negative effects of dams are exacerbated by increased drought periods and associated water withdrawals, especially in semi-arid regions. Stream fishes are particularly threatened owing to their mobile nature and requirement for multiple habitats to complete their life cycles. An understanding of relationships with fragmentation and flow regimes, particularly as coarse-scale (e.g. catchment) constraints on species distributions, is essential for stream fish conservation strategies. Prairie chub ( Macrhybopsis australis ) is a small-bodied minnow (Cyprinidae) with poorly understood ecology endemic to the North American Great Plains. Suspected declines in abundance and extirpations have resulted in conservation interest for prairie chub at state and federal levels. Prairie chub is thought to share its reproductive strategy with pelagic-broadcast spawning minnows (pelagophils). Freshwater pelagic-broadcast spawning fishes have been disproportionately affected by fragmentation and streamflow alteration globally. Relationships of prairie chub occurrence with coarse-scale fragmentation and streamflow metrics were examined in the upper Red River catchment. Occurrence probability was modelled using existing survey data, while accounting for variable detection. The modelled relationships were used to project the distribution of prairie chub in both a wet and dry climatic period. The probability of prairie chub occurrence was essentially zero at sites with higher densities of upstream dams, but increased sharply with increases in flow magnitude, downstream open mainstem, and flood duration. The projected distribution of prairie chub was broader than indicated by naïve occurrence, but similar in both climatic periods. The occurrence relationships are consistent with the hypotheses of pelagic broadcast spawning and represent coarse-scale constraints that are useful for identifying areas of the stream network with higher potential for finer-scale prairie chub conservation and recovery efforts. In addition to informing pelagophil conservation, the relationships are also applicable to pelagic-broadcast spawning fishes in marine environments.

Oklahoma, Texas↗
USGS2003

Preface: Phragmites australis: A sheep in wolf's clothing?

A. problem with national priorities for control or prevention of aquatic nuisance species is that we often do not know the full extent of the problem, if there is one. To address this issue, we hosted a technical forum and workshop-Phragmites australis: A Sheep in Wolf's Clothing?--with a focus on new research and critical reviews that address the role of Phragmites as a noxious weed. ... The Workshop helped focus the national effort in new multidisciplinary research to better understand the ecology of P australis and its ecosystem-level effects on the structure and function of coastal wetlands.

Estuaries↗
USGS2011

Stream-groundwater interactions

Streams and their surrounding catchments exchange water and solutes on a range of physical scales. Exchange with the stream may extend into the interstitial areas of the streambed, the hyporheic zone, the riparian area, or the catchment's groundwater flow system. Even at the smaller scales, the exchanges significantly influence solute transport, nutrient cycling, and the aquatic ecosystem. Over the recent decades, considerable attention has been given to the solute transport aspects of stream–groundwater interactions. Stream–groundwater interactions are now being recognized as practical matters to be considered in environmental issues, such as stream restoration and fish habitat. In this chapter, the emphasis is on introducing (1) the breadth of hydrologic interactions between streams and groundwater and (2) the importance of interpreting these interactions to understanding stream chemistry and ecology.

Book chapter↗
USGS2010

BRIDGES: Evolution of basic and applied linkages in benthic science

Growing awareness of environmental degradation resulted in stricter environmental regulations and laws for aquatic ecosystems. These regulations were followed by an increase in applied research and monitoring beginning in the early 1970s. The number of applied scientists who were members of the North American Benthological Society grew at a commensurate rate. The editors of J-NABS recognized that, despite these increases, submitted manuscripts mostly addressed basic science. In response, the BRIDGES section of J-NABS was created in 1994 to provide a forum for linking basic ecological principles to applied science problems and issues. We examined the emergence of applied science topics in J-NABS and its predecessor, Freshwater Invertebrate Biology , from their beginning in 1982 to 2009. We classified papers among 11 categories that included a basic/applied science linkage. In the 1980s, applied papers were predominantly on effects of eutrophication/pollution and landuse changes. When BRIDGES was established in 1994, papers were solicited by editors and BRIDGES sections usually included >1 paper on a common theme to express complementary or alternate viewpoints. Forty-two papers appeared in BRIDGES between 1994 and 2009, but the number per issue declined after 2001. The total number of applied science papers in J-NABS has increased since ∼1994. Citation analysis of BRIDGES papers illustrates how information is being cited, but applied papers often are used in ways that might not lead to citations. BRIDGES transitioned to a new format in September 2009 to address new types of complex, multifaceted linkages. All new BRIDGES articles will be open access, and authors will be encouraged to produce lay-language fact sheets and to post them on the web.

Journal of the North American Benthological Societ↗
USGS2023

U.S. Geological Survey science vision for native freshwater mussel research in the United States

Executive Summary North America is a global center for native freshwater mussel (order Unionida, hereinafter “mussels”) diversity, with more than 350 species. Mussels are among the most imperiled fauna on the planet. Reasons for both local and widespread declines in mussels are mostly unknown, although the threats may include habitat loss and fragmentation, diseases, environmental contaminants, altered flow regimes, migration barriers to larval hosts, non-native species, and climate change. Over the past three decades, research on mussels has been substantial. Nevertheless, current conservation and management efforts are limited by significant information gaps. For example, the effects of emerging stressors on mussels are largely unknown and identifying when habitats are rehabilitated and suitable for reestablishment of mussels remains challenging. Additionally, historical and current information on the distribution, taxonomy, and life histories are often unreliable or lacking altogether, and more reliable information is needed for many species. We identified focal research themes, goals, and objectives where research on mussels is needed based on information gaps identified through conversations with resource partners across local, regional, and national organizations. Research on biodiversity seeks to enhance the diversity of mussel species and populations to support healthy aquatic ecosystems. Research on emerging stressors seeks to improve the understanding of how mussel species, populations, and communities respond to emerging stressors, including environmental contaminants and climate change. Research on conservation seeks to enhance the recovery of species and populations and to identify data gaps limiting the conservation of mussels and their habitats. Mussels are in urgent need of proactive conservation because they are an integral part of our natural heritage, enhance biodiversity, and provide vital ecological services that support freshwater ecosystems. The U.S. Geological Survey (USGS) has been, and continues to be, a leader in mussel research. Although the USGS is well suited to address the broad-scale multidisciplinary research needed to conserve mussels, the USGS has had substantial loss of scientists with mussel expertise over the past 20 years. However, the breadth of the USGS expertise on mussels can be leveraged internally across other USGS mission and program areas and externally across research partners. Given the breadth and scope of the issues facing mussels across the United States, the research themes outlined in this science vision can only be accomplished through extensive collaborations between the USGS and the full spectrum of natural resource partners, including other Federal and State agencies, Tribal organizations, universities, industries, and nongovernmental organizations.

Circular↗
USGS2020

Water priorities for the Nation—U.S. Geological Survey Integrated Water Availability Assessments

The United States faces growing challenges to its water supply, infrastructure, and aquatic ecosystems because of population growth, climate change, floods and droughts, and aging water delivery systems. To help address these challenges, the U.S. Geological Survey (USGS) Water Resources Mission Area has established new strategic priorities that capitalize on the operational and scientific strengths of the USGS to address these complex societal issues. The USGS Integrated Water Availability Assessment Program within the Water Resources Mission Area will provide nationally consistent assessments of water available for human and ecological needs and identify factors that limit water availability. Integrated Water Availability Assessments will assess current conditions, long-term trends, factors responsible for current conditions and observed trends, and provide forecasts of future changes at national and regional scales.

Conterminous United States↗
USGS2017

Feeding ecology of Brook Silverside, Golden Shiner, and Subyearling Pumpkinseed in a Lake Ontario embayment

Fish feeding ecology has been shown to vary over a 24-h period in terms of the prey consumed and feeding intensity. Consequently, in order to best determine the interspecific feeding associations within a fish community, examination of the diet at multiple times over a 24-h period is often necessary. We examined the diel feeding ecology of three fish species that were numerically dominant in a Lake Ontario embayment during summer. The diet of each of the three species, young-of-year Pumpkinseed Lepomis gibbosus , Golden Shiner Notemigonus crysoleucas , and Brook Silverside Labidesthes sicculus , was distinct with no significant overlap in diet composition occurring within any of the 4-h time intervals. The diet composition of each species suggested that Brook Silverside were feeding at the surface (terrestrial invertebrates and aquatic surface dwelling hemipterans), whereas young-of-year Pumpkinseed (amphipods) and Golden Shiner (tipulids) were feeding on different benthic prey. Differences in feeding periodicity were most pronounced for young-of-year Pumpkinseed. Our findings provide valuable insights on interspecific feeding associations among these three fish species during summer in a Lake Ontario embayment.

Journal of Fish and Wildlife Management↗
USGS2013

Integrated carbon budget models for the Everglades terrestrial-coastal-oceanic gradient: Current status and needs for inter-site comparisons

Recent studies suggest that coastal ecosystems can bury significantly more C than tropical forests, indicating that continued coastal development and exposure to sea level rise and storms will have global biogeochemical consequences. The Florida Coastal Everglades Long Term Ecological Research (FCE LTER) site provides an excellent subtropical system for examining carbon (C) balance because of its exposure to historical changes in freshwater distribution and sea level rise and its history of significant long-term carbon-cycling studies. FCE LTER scientists used net ecosystem C balance and net ecosystem exchange data to estimate C budgets for riverine mangrove, freshwater marsh, and seagrass meadows, providing insights into the magnitude of C accumulation and lateral aquatic C transport. Rates of net C production in the riverine mangrove forest exceeded those reported for many tropical systems, including terrestrial forests, but there are considerable uncertainties around those estimates due to the high potential for gain and loss of C through aquatic fluxes. C production was approximately balanced between gain and loss in Everglades marshes; however, the contribution of periphyton increases uncertainty in these estimates. Moreover, while the approaches used for these initial estimates were informative, a resolved approach for addressing areas of uncertainty is critically needed for coastal wetland ecosystems. Once resolved, these C balance estimates, in conjunction with an understanding of drivers and key ecosystem feedbacks, can inform cross-system studies of ecosystem response to long-term changes in climate, hydrologic management, and other land use along coastlines

Florida↗
USGS2014

Natural flow regimes of the Ozark-Ouachita Interior Highlands region

Natural flow regimes represent the hydrologic conditions to which native aquatic organisms are best adapted. We completed a regional river classification and quantitative descriptions of each natural flow regime for the Ozark–Ouachita Interior Highlands region of Arkansas, Missouri and Oklahoma. On the basis of daily flow records from 64 reference streams, seven natural flow regimes were identified with mixture model cluster analysis: Groundwater Stable, Groundwater, Groundwater Flashy, Perennial Runoff, Runoff Flashy, Intermittent Runoff and Intermittent Flashy. Sets of flow metrics were selected that best quantified nine ecologically important components of these natural flow regimes. An uncertainty analysis was performed to avoid selecting metrics strongly affected by measurement uncertainty that can result from short periods of record. Measurement uncertainties (bias, precision and accuracy) were assessed for 170 commonly used flow metrics. The ranges of variability expected for select flow metrics under natural conditions were quantified for each flow regime to provide a reference for future assessments of hydrologic alteration. A random forest model was used to predict the natural flow regimes of all stream segments in the study area based on climate and catchment characteristics, and a map was produced. The geographic distribution of flow regimes suggested distinct ecohydrological regions that may be useful for conservation planning. This project provides a hydrologic foundation for future examination of flow–ecology relationships in the region. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Arkansas, Missouri, Oklahoma↗
USGS2016

Applications of genetic data to improve management and conservation of river fishes and their habitats

Environmental variation and landscape features affect ecological processes in fluvial systems; however, assessing effects at management-relevant temporal and spatial scales is challenging. Genetic data can be used with landscape models and traditional ecological assessment data to identify biodiversity hotspots, predict ecosystem responses to anthropogenic effects, and detect impairments to underlying processes. We show that by combining taxonomic, demographic, and genetic data of species in complex riverscapes, managers can better understand the spatial and temporal scales over which environmental processes and disturbance influence biodiversity. We describe how population genetic models using empirical or simulated genetic data quantify effects of environmental processes affecting species diversity and distribution. Our summary shows that aquatic assessment initiatives that use standardized data sets to direct management actions can benefit from integration of genetic data to improve the predictability of disturbance–response relationships of river fishes and their habitats over a broad range of spatial and temporal scales.

Fisheries↗
USGS2017

Historical analysis of riparian vegetation change in response to shifting management objectives on the Middle Rio Grande

Riparian ecosystems are valuable to the ecological and human communities that depend on them. Over the past century, they have been subject to shifting management practices to maximize human use and ecosystem services, creating a complex relationship between water policy, management, and the natural ecosystem. This has necessitated research on the spatial and temporal dynamics of riparian vegetation change. The San Acacia Reach of the Middle Rio Grande has experienced multiple management and river flow fluctuations, resulting in threats to its riparian and aquatic ecosystems. This research uses remote sensing data, GIS, a review of management decisions, and an assessment of climate to both quantify how riparian vegetation has been altered over time and provide interpretations of the relationships between riparian change and shifting climate and management objectives. This research focused on four management phases from 1935 to 2014, each highlighting different management practices and climate-driven river patterns, providing unique opportunities to observe a direct relationship between river management, climate, and riparian response. Overall, we believe that management practices coupled with reduced surface river-flows with limited overbank flooding influenced the compositional and spatial patterns of vegetation, including possibly increasing non-native vegetation coverage. However, recent restoration efforts have begun to reduce non-native vegetation coverage.

New Mexico↗
USGS2004

Physical aquatic habitat assessment data, Ozark plateaus, Missouri and Arkansas

This report presents data from two related studies on physical habitat in small streams in the Ozark Plateaus Physiographic Province of Missouri and Arkansas. Seventy stream reaches and their contributing drainage basins were assessed using a physical habitat protocol designed to optimize understanding of how stream reach characteristics relate to drainage-basin characteristics. Drainage-basin characteristics were evaluated using geographic information system (GIS) techniques and datasets designed to evaluate the geologic, physiographic, and land-use characteristics of encompassing drainage basins. Reach characteristics were evaluated using a field-based geomorphology and habitat protocol. The data are intended to complement ecological studies on Ozark Plateaus streams.

Data Series↗
USGS1998

Vulnerability to predation and physiological stress responses in juvenile chinook salmon ( Oncorhynchus tshawytscha ) experimentally infected with Renibacterium salmoninarum

We experimentally infected juvenile chinook salmon ( Oncorhynchus tshawytscha ) with Renibacterium salmoninarum (Rs), the causative agent of bacterial kidney disease (BKD), to examine the vulnerability to predation of fish with differing levels of Rs infection and assess physiological change during progression of the disease. Immersion challenges conducted during 1992 and 1994 produced fish with either a low to moderate (1992) or high (1994) infection level of Rs during the 14-week postchallenge rearing period. When equal numbers of treatment and unchallenged control fish were subjected to predation by either northern squaw fish ( Ptychocheilus oregonensis ) or smallmouth bass ( Micropterus dolomieui) , Rs-challenged fish were eaten in significantly greater numbers than controls by nearly two to one. In 1994, we also sampled fish every 2 weeks after the challenge to determine some stressful effects of Rs infection. During disease progression in fish, plasma cortisol and lactate increased significantly whereas glucose decreased significantly. Our results indicate the role that BKD may play in predator-prey interactions, thus ascribing some ecological significance to this disease beyond that of direct pathogen-related mortality. In addition, the physiological changes observed in our fish during the chronic progression of BKD indicate that this disease is stressful, particularly during the later stages.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2018

Effect of climate change on disease spread in wildlife

A growing body of evidence indicates that climate change alone, or acting synergistically with current anthropogenic threats, is affecting the health of wild populations of aquatic and terrestrial wildlife. Measurable by-products of climate change include elevated atmospheric concentrations of greenhouse gases, higher average global temperatures; variations in global precipitation patterns, rising and warming oceans, altered hydrographs of rivers, and increased mid-continental drying during summer. These consequences affect the terrestrial environment through shifts in phenology, vegetation cover, and fire regimes. Warmer ocean temperatures, increased acidification, rise in sea levels, and reduction in sea ice cover are also leading to widespread ecological changes in marine systems. Wildlife populations face a variety of climate-related pressures, such as changes in animal distribution or density, limitation of food resources, and alteration to critical habitats. The increased potential for emergence and resurgence of diseases that are responsive to environmental conditions also has implications for wildlife populations. Shifts in temperature or other climatic factors may directly affect the incidence of disease in wildlife by altering host-pathogen interactions, promoting vector populations or allowing new ranges for vectors, or reducing development times for parasites. A number of examples from both field and laboratory studies have demonstrated a clear link between warming environments and disease spread. Many climate-related environmental changes also influence wildlife health indirectly. For example, increasing temperatures, in combination with shifts in rainfall and humidity, may aggravate current trends for water resource limitation and habitat degradation or destruction and lead to increased crowding of animal populations, thereby promoting transmission opportunities of pathogens within populations or across species. Although it may be difficult to disentangle the influences of other anthropogenic changes from the direct effects of warming, some ecosystems provide especially useful models for studying climate-related disease spread in wildlife. For example, the effects of climate change on parasite dynamics may be easily observed in the Arctic, where environmental changes are occurring rapidly, anthropogenic influences are relatively limited, and biodiversity is generally low. Marine ecosystems are also undergoing rapid rates of change and may be vulnerable to a variety of natural and anthropogenic perturbations. Although many factors affect the health of organisms in ocean environments, temperature has been clearly linked to an increase in disease prevalence among sessile organisms such as corals. In this chapter, we discuss observed and predicted changes to wildlife health resulting from climate change. Our review will not include all aspects of wildlife health, but will instead focus on established or suspected links between climate drivers and disease spread and discuss examples from the current literature. Here, we define disease spread to include: 1) change in geographical or altitudinal distribution of pathogens, parasites, and vectors and the diseases they cause; 2) change in prevalence or severity of disease; and 3) emergence of novel diseases. Additionally, because wildlife species serve as reservoirs for zoonotic diseases that affect both animals and humans, we include select examples of the effect of climate change on the capacity of wildlife to harbor and spread these disease agents.

Book chapter↗
USGS2019

Drought in the U.S. Caribbean: Impacts to freshwater ecosystems

Healthy and functioning freshwater ecosystems are needed for successful conservation and management of native fish and invertebrate species, and the services they provide to human communities, across the U.S. Caribbean. Yet streams, rivers, and reservoirs are vulnerable to the effects of extreme weather events, urbanization, energy and water development, and other environmental and human-caused disturbances (Neal et al., 2009). One major management concern is the impact of prolonged drought on freshwater ecosystems. Drought impacts streamflow, dissolved oxygen content, water quality, stream connectivity, available habitat, and other important freshwater habitat characteristics necessary for sustaining fish and invertebrate populations (Covich et al., 2006). These changes can impact species interactions, abundance, life history events, and the presence of native and non-native species (Larsen, 2000; Covich et al., 2006; Ramírez et al., 2018). Drought impacts aquatic ecosystems and species both in the short-term and long-term, depending on the severity and duration of the event (e.g. Covich et al., 2006 ). In Puerto Rico, all native freshwater fish, shrimp, and snail species spend part of their lives in estuarine and marine ecosystems and depend on being able to move between these habitats to survive, so maintaining connectivity is key (e.g., Engman et al., 2017 ). Freshwater ecosystems also provide recreational, cultural, and ecological value to humans ( Kwak et al., 2007 ; Neal et al., 2009 ). For example, some communities in Puerto Rico engage in artisanal shrimp and freshwater crab fishing ( Neal et al., 2009 ). Artisanal fishing for postlarvae gobioids, known colloquially as “cetí” also occurs at the river mouths of large drainages and has strong cultural significance in parts of Puerto Rico, such as Arecibo (Kwak et al., 2016). The U.S. Virgin Islands (USVI) is particularly sensitive to drought, because almost all streams are ephemeral and typically only flow after rainfall. These intermittent channels, known locally as “ghuts”, run down the surface of steep slopes, rather than through the ground, and are important sources of freshwater. Natural springs are often located in ghuts and can form pools of freshwater that serve as habitat for wetland and migratory birds, freshwater shrimp and fish, and amphibians ( Nemeth and Platenburg, 2007 ; Gardner, 2008 ).

Puerto Rico, U.S. Virgin Islands↗
USGS2023

Evaluation of threatened, endangered, and rare fish species and communities of the St. Lawrence River and its tributaries in the United States

Biodiversity is responsible for important ecological processes like productivity and ecosystem stability, and rare species are a major component of biodiversity. Rarity increases a species' vulnerability to disturbances and also makes them difficult to study. Globally, species of freshwater systems are some of the most threatened, and evaluation of rare freshwater species and their habitats is needed to help preserve natural flexibility and ecological function. We conducted an analysis of full fish communities of the upper St. Lawrence River and its major US tributaries, with the goals of determining species locations and abundances, associated environmental conditions, the distribution of distinct fish assemblages across the landscape (with emphasis on communities supporting rare species), and potential threats. From 2009 to 2015, the US Geological Survey (USGS) and Saint Regis Mohawk Tribe (SRMT) worked together using standardized methods to collect community samples within 4 different aquatic realms (shallow and deep lentic, and small and large lotic systems) and determine species-specific fish abundances, frequencies of occurrence, and associated habitat signatures and spatial distributions. Distinct fish assemblages and associated habitat conditions were objectively identified by multivariate and hypothesis-testing methods. We used a geographic information system (GIS) to spatially associate habitat, biotic, and landscape attributes within each stream reach throughout the study area, facilitating quantification of distribution patterns. Comparisons with historical data provided estimates of loss or gain of threatened and endangered species (T&E) colonies. We developed a disturbance index to highlight potential threats to aquatic species. More than 140,000 fishes of 87 species were collected from a total of 1140 sample sites, covering 278 stream reaches, including the endangered Notropis anogenus (Pugnose Shiner), and threatened Hiodon tergisus (Mooneye), Etheostoma pellucidum (Eastern Sand Darter), and Acipenser fulvescens (Lake Sturgeon). We identified 50 distinct fish assemblages differing in species composition, abundance, and/or diversity, but only 13 of those assemblages included a T&E species. The rareness, extent, and patchiness of fish assemblages created a mosaic of fish communities across the landscape, from headwaters to the mainstem of the St. Lawrence River. Comparisons with historic surveys (1978–2008) showed a stable number of T&E species colonies or an increase for some species. The geographic distribution of multimetric disturbance index values showed where combinations of disturbances to fish habitats might affect rare fish species and aquatic communities in the region. The species–habitat associations and fish assemblage distributions can be used for evaluation of species, communities, or habitats that may need protection or restoration.

St. Lawrence River study area↗