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USGS2025

Preparation and analysis methods for fish tissue collected from Lake Koocanusa, Montana

Lake Koocanusa, a reservoir, receives mine wastes from metallurgical coal mines in the Elk River Valley of British Columbia, Canada. Selenium and other elements discharged by the mines into the waters of the United States can pose unknown risks to aquatic life. The U.S. Geological Survey Wyoming-Montana Water Science Center can collaborate with Montana Fish, Wildlife and Parks and other State and Federal agencies to design studies and to collect fish tissues to help fill this knowledge gap. This report describes the processes, techniques, and methods used to collect and analyze fish tissue collected from Lake Koocanusa; and procedures used to review and manage data, including quality assurance and quality control procedures used by the U.S. Geological Survey Wyoming-Montana Water Science Center and supporting analytical laboratories. These fish tissue collections began in 2021.

Montana↗
USGS2025

Environmental characteristics of select managed ponds in the Sacramento–San Joaquin Delta—Implications for native fish conservation and research

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpose of our study was to examine the physiochemical and biological characteristics of select managed ponds in the Delta to determine if they would be suitable habitats for research involving the conservation of delta smelt ( Hypomesus transpacificus ). We studied 10 managed ponds distributed across the central part of the Delta situated on Bacon Island and Bouldin Island in San Joaquin County, and Holland Tract and Webb Tract islands in Contra Costa County. The managed ponds had a diversity of physical habitat configurations and were not directly connected to waterways surrounding the islands and, therefore, not affected by tides. We studied the managed ponds from approximately November 2021 to December 2023 to assess water quality, zooplankton, fish, and pesticide metrics. Water levels in the managed ponds were managed to varying degrees and were mostly independent of climate-driven wet-dry seasonality. Water quality conditions varied among ponds and were independent of geographic location. Overall, mean monthly chlorophyll a concentration ranged from 15 to 57 (mean=30) micrograms per liter (μg/L), dissolved oxygen concentration ranged from 4 to 9 (mean=7) milligrams per liter (mg/L), pH was 8, salinity was 1 practical salinity units (PSU), specific conductance ranged from 1,202 to 1,839 (mean=1,471) microsiemens per centimeter (μS/cm), and turbidity ranged from 13 to 24 (mean=19) Formazin Nephelometric Units (FNU). Water temperature thresholds that contribute to stress (21 degrees Celsius [°C]) and mortality (28 °C) of delta smelt were often exceeded during summer and fall, though vertical stratification contributed to lower bottom temperatures in the deepest managed ponds, which could potentially provide thermal refugia for delta smelt so long as dissolved oxygen concentrations are suitable. Zooplankton populations were broadly similar among managed ponds and included calanoid and cyclopoid copepods that would be suitable prey for delta smelt. Overall average total zooplankton biomass, as measured with a Schindler-Patalas trap, was 0.6 μg/L (min=0, max=63.6) and peaked during spring at more than 4 μg/L. Fish populations highly varied among the managed ponds with potential predators of delta smelt such as largemouth bass ( Micropterus salmoides ) and black crappie ( Pomoxis nigromaculatus ) present in several of the managed ponds; predator distribution among ponds seemed to have been driven primarily by deliberate stocking to facilitate local fisheries. Measured pesticide concentrations were below U.S. Environmental Protection Agency Aquatic Life Benchmarks except for exceedances of three compounds (diuron [herbicide], clothianidin [insecticide], and deltamethrin [pyrethroid insecticide]) in samples collected from ponds on Bouldin Island and Webb Tract. Overall, most managed ponds seemed suitable to support delta smelt, though physical control of potential predators and summer temperature might be needed. The results provide guidance on how to engineer and manage new managed ponds to support research and conservation efforts for delta smelt and other native fishes.

California↗
USGS2005

The fishes of George Washington Carver National Monument, Missouri, 2003

Fish were collected at six sites at George Washington Carver National Monument by seining and electrofishing during a base-flow period on July 17-18, 2003. Approximately 700 fish were collected and identified at the six sampling sites. Those individuals represented 17 species (and 1 hybrid) and 13 genera. The number of species collected at the five stream sites ranged from 9 to 12; a hybrid sunfish and 4 species were collected from a pond. Fish collected at stream sites were typical of small headwater streams and no species collected in this study are federally-listed threatened or endangered species. The three most common species were the southern redbelly dace, central stoneroller, and green sunfish. Some differences existed between the assemblages (groups of species) collected in 2003 and in the previous inventories. Four of the 17 fish species collected in this inventory previously had not been collected at the monument. However, 11 species collected in one or more of the previous inventories were not collected in this effort. There is no indication that a change in environmental conditions is responsible for the absence of these species; more likely reasons are seasonal variability, extirpation, low population density, and misidentification. Four species collected at George Washington Carver National Monument may be of special interest to National Park Service managers and others. The cardinal shiner and stippled darter are endemic to the Ozark Plateaus. The Arkansas darter is considered a species of conservation concern by the State of Missouri. The grass carp is an introduced species.

Scientific Investigations Report↗
USGS2005

Seepage investigation on selected reaches of Fish Creek, Teton County, Wyoming, 2004

A seepage investigation was conducted on Fish Creek, a tributary to the Snake River in Teton County in western Wyoming, near Wilson. Mainstem, return flow, tributary, spring, and diversion sites were selected and measured on six reaches along Fish Creek. Flow was measured under two flow regimes, high flow in August 2004 and base flow in November 2004. During August 17-19, 2004, 20 sites had quantifiable discharge with median values ranging from 0.93 to 384 ft3/s for the 14 mainstem sites on Fish Creek, and from 0.35 to 12.2 ft3/s for the 5 return, spring, and tributary sites (inflows). The discharge was 2.23 ft3/s for the single diversion site (outflow). Estimated gains or losses from ground water were calculated for all reaches using the median discharge values and the estimated measurement errors. Reach 1 had a calculated gain in discharge from ground water (23.8 ?3.3 ft3/s). Reaches 2-6 had no calculated gains in flow, greater than the estimated error, that could be attributed to ground water. A second set of measurements were made under base-flow conditions during November 3-4, 2004. Twelve of the 20 sites visited in August 2004 were flowing and were measured. All of the Reach 1 sites near Teton Village were dry. Median discharge values ranged from 10.3 to 70.0 ft3/s on the nine Fish Creek mainstem sites, and from 2.32 to 3.71 ft3/s on the three return, spring, and tributary sites (inflows). Reaches 2, 3 and 6 had a gain from ground water. Reaches 4 and 5 had no calculated gains in flow, greater than the estimated error, that could be attributed to ground water.

Scientific Investigations Report↗
USGS2010

Evaluating effects of potential changes in streamflow regime on fish and aquatic-invertebrate assemblages in the New Jersey Pinelands

Changes in water demand associated with population growth and changes in land-use practices in the Pinelands region of southern New Jersey will have a direct effect on stream hydrology. The most pronounced and measurable hydrologic effect is likely to be flow reductions associated with increasing water extraction. Because water-supply needs will continue to grow along with population in the Pinelands area, the goal of maintaining a sustainable balance between the availability of water to protect existing aquatic assemblages while conserving the surficial aquifer for long-term support of human water use needs to be addressed. Although many aquatic fauna have shown resilience and resistance to short-term changes in flows associated with water withdrawals, sustained effects associated with ongoing water-development processes are not well understood. In this study, the U.S. Geological Survey sampled forty-three 100-meter-long stream reaches during high- and low-flow periods across a designed hydrologic gradient ranging from small- (4.1 square kilometers (1.6 square miles)) to medium- (66.3 square kilometers (25.6 square miles)) sized Pinelands stream basins. This design, which uses basin size as a surrogate for water availability, provided an opportunity to evaluate the possible effects of potential variation in stream hydrology on fish and aquatic-invertebrate assemblage response in New Jersey Pinelands streams where future water extraction is expected based on known build-out scenarios. Multiple-regression models derived from extracted non-metric multidimensional scaling axis scores of fish and aquatic invertebrates indicate that some variability in aquatic-assemblage composition across the hydrologic gradient is associated with anthropogenic disturbance, such as urbanization, changes in stream chemistry, and concomitant changes in high-flow runoff patterns. To account for such underlying effects in the study models, any flow parameter or assemblage attribute that was found to be significantly correlated (|rho| = 0.5000) to known anthropogenic drivers (for example, the amount of urbanization in the basin) was eliminated from analysis. A reduced set of low- and annual-flow hydrologic variables, found to be unrelated to anthropogenic influences, was used to develop assemblage-response models. Many linear (monotonic) and curvilinear bivariate flow-ecology response models were developed for fish and invertebrate assemblages. For example, the duration and magnitude of low-flow events were significant predictors of invertebrate-assemblage complexity (for example, invertebrate-species richness, Plecoptera richness, and Ephemeroptera abundance); however, response models between flow attributes and fish-assemblage structure were, in all cases, more poorly fit. Annual flow variability also was important, especially variability across mean minimum monthly flows and annual mean streamflow. In general, all response models followed upward or downward trends that would be expected given hydrologic changes in Pinelands streams. This study demonstrates that the structural and functional response of aquatic assemblages of the Pinelands ecosystem resulting from changes in water-use practices associated with population growth and increased water extraction may be predictable.

Scientific Investigations Report↗
USGS2011

TOPMODEL simulations of streamflow and depth to water table in Fishing Brook Watershed, New York, 2007-09

TOPMODEL, a physically based, variable-source area rainfall-runoff model, was used to simulate streamflow and depth to water table for the period January 2007-September 2009 in the 65.6 square kilometers of Fishing Brook Watershed in northern New York. The Fishing Brook Watershed is located in the headwaters of the Hudson River and is predominantly forested with a humid, cool continental climate. The motivation for applying this model at Fishing Brook was to provide a simulation that would be effective later at this site in modeling the interaction of hydrologic processes with mercury dynamics. TOPMODEL uses a topographic wetness index computed from surface-elevation data to simulate streamflow and subsurface-saturation state, represented by the saturation deficit. Depth to water table was computed from simulated saturation-deficit values using computed soil properties. In the Fishing Brook Watershed, TOPMODEL was calibrated to the natural logarithm of streamflow at the study area outlet and depth to water table at Sixmile Wetland using a combined multiple-objective function. Runoff and depth to water table responded differently to some of the model parameters, and the combined multiple-objective function balanced the goodness-of-fit of the model realizations with respect to these parameters. Results show that TOPMODEL reasonably simulated runoff and depth to water table during the study period. The simulated runoff had a Nash-Sutcliffe efficiency of 0.738, but the model underpredicted total runoff by 14 percent. Depth to water table computed from simulated saturation-deficit values matched observed water-table depth moderately well; the root mean squared error of absolute depth to water table was 91 millimeters (mm), compared to the mean observed depth to water table of 205 mm. The correlation coefficient for temporal depth-to-water-table fluctuations was 0.624. The variability of the TOPMODEL simulations was assessed using prediction intervals grouped using the combined multiple-objective function. The calibrated TOPMODEL results for the entire study area were applied to several subwatersheds within the study area using computed hydrogeomorphic properties of the subwatersheds.

Scientific Investigations Report↗
USGS2017

Hydraulic and biological analysis of the passability of select fish species at the U.S. Geological Survey streamgaging weir at Blackwells Mills, New Jersey

Recent efforts to advance river connectivity for the Millstone River watershed in New Jersey have led to the evaluation of a low-flow gauging weir that spans the full width of the river. The methods and results of a desktop modelling exercise were used to evaluate the potential ability of three anadromous fish species ( Alosa sapidissima [American shad], Alosa pseudoharengus [alewife], and Alosa aestivalis [blueback herring]) to pass upstream over the U.S. Geological Survey Blackwells Mills streamgage (01402000) and weir on the Millstone River, New Jersey, at various streamflows, and to estimate the probability that the weir will be passable during the spring migratory season. Based on data from daily fishway counts downstream from the Blackwells Mills streamgage and weir between 1996 and 2014, the general migratory period was defined as April 14 to May 28. Recorded water levels and flow data were used to theoretically estimate water depths and velocities over the weir, as well as flow exceedances occurring during the migratory period. Results indicate that the weir is a potential depth barrier to fish passage when streamflows are below 200 cubic feet per second using a 1-body-depth criterion for American shad (the largest fish among the target species). Streamflows in that range occur on average 35 percent of the time during the migratory period. An increase of the depth criterion to 2 body depths causes the weir to become a possible barrier to passage when flows are below 400 cubic feet per second. Streamflows in that range occur on average 73 percent of the time during the migration season. Average cross-sectional velocities at several points along the weir do not seem to be limiting to the fish migration, but maximum theoretical velocities estimated without friction loss over the face of the weir could be potentially limiting.

New Jersey↗
USGS2020

Effects of box culverts on stream habitat, channel morphology, and fish and macroinvertebrate communities at selected sites in South Carolina, 2016–18

Much attention has been placed on the role that under-roadway culverts may have in inhibiting upstream fish movement because of altered hydrology and unsuitable conditions for accessing or swimming through the culvert. Other culvert effects related to habitat alterations or disturbance to macroinvertebrate communities have received relatively little attention. Entities responsible for culverts or other stream crossing structures are required to follow the U.S. Army Corps of Engineers guidelines for compensatory mitigation should any disturbance result from an engineering activity. One factor considered in the scoring of mitigation requirements is culvert length. Except for shading a longer length of stream, it is unknown whether longer culverts result in greater disturbance to stream habitat or the biotic communities than shorter culverts. The U.S. Geological Survey, in cooperation with the South Carolina Department of Transportation, evaluated the role of culverts in altering physical habitat and community structure of fish and macroinvertebrates at 20 sites in South Carolina. Culvert sites were categorized by length (either greater than 30.5 meters or less than or equal to 30.5 meters) and physiographic province (Piedmont or upper Coastal Plain). This study design allowed for a regional assessment to determine if culverts may have different effects on habitat and biotic communities in different physical settings. The results indicated considerable variation in physical habitat characteristics within and among the culvert sites from all categories. A consistent finding was that channel cross-sectional area tended to increase in reaches downstream from culverts in the upper Coastal Plain. The primary dimension of change was vertical, that is, incision of the streambed. This change, however, did not seem to coincide with a deleterious effect on the fish community. Increased habitat complexity and greater taxonomic richness were observed at most sites with downstream incision. Macroinvertebrate communities were highly variable and did not tend to cluster along any of the culvert categories, which may reflect the variability of microhabitats within each site. In contrast, fish communities were largely segregated by physiographic province but did not show any other significant clustering on the basis of upstream or downstream reach or culvert length. Given the small within-group sample size, extrapolation of results should be done carefully, acknowledging the physiographic and group characteristics.

South Carolina↗
USGS2026

Analysis of alternative weir designs for improved passage of select fish at the U.S. Geological Survey streamgaging weir at Blackwells Mills, New Jersey

As the population of New Jersey continues to remain dense, the need for water supply will likely continue to be high, which can lead to water managers needing to make difficult decisions about managing drinking-water supply. Streamgaging weirs like the ones used by the U.S. Geological Survey (USGS) play a critical role in providing accurate and stable streamflow data, but their presence can affect the passage of diadromous fish species such as river herring ( Alosa pseudoharengus [alewife], Alosa aestivalis [blueback herring], and Alosa sapidissima [American shad]). In some situations, weirs existing in rivers and streams are no longer used because they were part of a farm irrigation system or some type of industrial operation. The weir at the USGS streamgage 01402000 Millstone River at Blackwells Mills, New Jersey, was purposefully built as a hydraulic-control structure that provides a precise and stable control for the measurement of stage and computation of continuous streamflow. To satisfy the dual need of maintaining accurate streamflow data and providing improved fish passage for select species of fish during migration season, the USGS proposed the development and evaluation of two alternative weir designs that would meet the criteria established for successful passage of American shad, alewife, and blueback herring during their yearly migration. The designs were also required to maintain adequate control of the upstream pool elevation necessary for the precise computation of streamflow used by State agencies for municipal water-supply purposes for surrounding communities. Two alternative weir design modifications were incorporated at the center of the Blackwells Mills weir and modeled using two-dimensional hydraulic modeling software and three-dimensional computational fluid-dynamics software to simultaneously evaluate conditions for passage of the target fish species and effects to streamflow computations at the streamgage. The models were calibrated to existing conditions around the weir location using surveyed-elevation data and recorded stage, streamflow, and velocity in the Millstone River. The alternative weir designs lowered the weir crest by 1.02 feet (ft) and the resulting simulations showed an effective increase in depth of 0.98 ft at the median streamflow of 251 cubic feet per second (ft 3 /s) and 0.96 ft at the 95-percent exceedance streamflow of 98 ft 3 /s. The alternative weir designs were also found to increase streamflow depth across the shallowest portions of the weir structure at the downstream anti-scour skirt by lowering the skirt about 4 inches, allowing for two or more body depths of water for American shad, alewife, and blueback herring at the median migration streamflow of 251 ft 3 /s. The alternative weir designs also reduced the highest stream velocities across the downstream weir sill and anti-scour skirt from about 9 to 10 feet per second, and the depth-averaged velocity to about 7 to 8 feet per second. The sensitivity of the weir with respect to the computation of streamflow was increased from about 1.8 cubic feet per second per hundredth foot to 1.6 cubic feet per second per hundredth foot for streamflows of about 10–100 cubic feet per second.

New Jersey↗
USGS2003

Baseline assessment of fish communities, benthic macroinvertebrate communities, and stream habitat and land use, Big Thicket National Preserve, Texas, 1999-2001

The Big Thicket National Preserve comprises 39,300 hectares in the form of nine preserve units connected by four stream corridor units (with two more corridor units proposed) distributed over the lower Neches and Trinity River Basins of southeastern Texas. Fish and benthic macroinvertebrate data were collected at 15 stream sites (reaches) in the preserve during 1999–2001 for a baseline assessment and a comparison of communities among stream reaches. The fish communities in the preserve were dominated by minnows (family Cyprinidae) and sunfishes (family Centrarchidae). Reaches with smaller channel sizes generally had higher fish species richness than the larger reaches in the Neches River and Pine Island Bayou units of the preserve. Fish communities in geographically adjacent reaches were most similar in overall community structure. The blue sucker, listed by the State as a threatened species, was collected in only one reach—a Neches River reach a few miles downstream from the Steinhagen Lake Dam. Riffle beetles (family Elmidae) and midges (family Chironomidae) dominated the aquatic insect communities at the 14 reaches sampled for aquatic insects in the preserve. The Ephemeroptera, Plecoptera and Trichoptera (EPT) Index, an index sensitive to water-quality degradation, was smallest at the Little Pine Island Bayou near Beaumont reach that is in a State 303(d)-listed stream segment on Little Pine Island Bayou. Trophic structure of the aquatic insect communities is consistent with the river continuum concept with shredder and scraper insect taxa more abundant in reaches with smaller stream channels and filter feeders more abundant in reaches with larger channels. Aquatic insect community metrics were not significantly correlated to any of the stream-habitat or land-use explanatory variables. The percentage of 1990s urban land use in the drainage areas upstream from 12 bioassessment reaches were negatively correlated to the reach structure index, which indicates less stable habitat for aquatic biota.

Texas↗
USGS2004

Assessment of Fish Habitat, Water Quality, and Selected Contaminants in Streambed Sediments in Noyes Slough, Fairbanks, Alaska, 2001-2002

During 2001-2002, the U.S. Geological Survey sampled streambed sediment at 23 sites, measured water quality at 26 sites, and assessed fish habitat for the entire length of Noyes Slough, a 5.5-mile slough of the Chena River in Fairbanks, Alaska. These studies were undertaken to document the environmental condition of the slough and to provide information to the public for consideration in plans to improve environmental conditions of the waterway. The availability of physical habitat for fish in the slough does not appear to be limited, although some beaver dams and shallow water may restrict movement, particularly during low flow. Elevated water temperatures in summer and low dissolved-oxygen concentrations are the principle factors adversely affecting water quality in Noyes Slough. Increased flow mitigated poor water-quality conditions and reduced the number of possible fish barriers. Flow appears to be the most prominent mechanism shaping water quality and fish habitat in Noyes Slough. Streambed sediment samples collected at 23 sites in 2001 were analyzed for 24 trace elements. Arsenic, lead, and zinc were the only trace elements detected in concentrations that exceed probable effect levels for the protection of aquatic life. The background concentration for arsenic in Noyes Slough is naturally elevated because of significant concentrations of arsenic in local bedrock and ground water. Sources of the zinc and lead contamination are uncertain, however both lead and zinc are common urban contaminants. Streambed-sediment samples from 12 sites in 2002 were analyzed for organochlorine pesticides, polychlorinated biphenyls (PCBs), and semivolatile organic compounds (SVOCs). The concentration of bis(2-ethylhexyl)phthalate of 2,600 micrograms per kilogram (?g/kg) for one sample from the site above Aurora Drive approached the aquatic-life criterion of 2,650 ?g/kg. Low concentrations of p-cresol, chrysene, and fluoranthene were detected in most of the sediment samples. The presence of these compounds in Noyes Slough sediment was expected because cresols are emitted to the atmosphere in the exhaust from motor vehicles and chrysene and fluoranthene are formed during the incomplete burning of coal, oil, gas, wood, garbage, or other organic substances. Low-level concentrations of DDT or its degradation products DDD and DDE were detected in all samples collected during 2002. However, total DDT (DDT+DDD+DDE) concentrations are less than the effects range median aquatic-life criterion of 46.1 ?g/kg. In general, total DDT concentrations were less than 10 ?g/kg, except for samples from two sites that have estimated concentrations of about 14 and 20 ?g/kg.

Water-Resources Investigations Report↗
USGS1987

The relation of streamflow to habitat for anadromous fish in the Stillaguamish River basin, Washington

The techniques of Instream Flow Incremental Methodology were used to determine the habitat available over a range of simulated streamflows for anadromous fish in certain reaches of streams in the Stillaguamish River basin, Washington. The stream discharge-habitat relations were used to identify that discharge termed the optimum discharge, which provides maximum habitat, for a particular species and life stage of fish. Optimum discharges varied throughout the Stillaguamish River basin because each discharge-habitat relation was unique. The mainstem of the Stillaguamish River is used primarily as a migration route by anadromous fish, but it is also used by chinook and coho salmon and steelhead trout for rearing and by steelhead adults and pink salmon for spawning. Optimum discharges, in cu ft/sec, ranged as follows in the mainstem Stillaguamish River: chinook fry, 600; steelhead--juveniles, 1,000, adults, 2,000, coho juveniles, 400; and pink spawning, 800. The North Fork Stillaguamish River is used for spawning and rearing by all the study fish species. Optimum discharges there were: chinook--spawning, 500 to 1,300, fry, 150 to 400; coho--spawning , 500 to 700, juveniles and fry, 50 to 200; steelhead--adults, 500 to 1,170, spawning, 800 to 900, fry, 50 to 140, juveniles, 300 to 500, chum spawning, 200 to 600; pink spawning, 300 to 600. All the study species spawn and rear in the South Fork Stillaguamish River, but coho spawn and rear fry only at the most upstream study site and chum spawn only at the most downstream site. Optimum discharge ranges on the South Fork were: chinook--spawning, 300 to 900, fry, 70 to 300; coho juveniles, 50 to 100; steelhead--adults, 300 to 900; spawning, 250 to 1,200, fry, 45 to 1,600, juveniles 200 to 500, pink spawning, 100 to 1,200; coho--spawning, 140, fry, 50; chum spawning, 100. Four tributary streams are used by all species except Pilchuck and Canyon Creeks, which are not used by chum salmon. Optimum discharges for all tributary streams ranged as follows: chinook--spawning, 170 to 750, fry 50 to 170; coho--spawning, 90 to 350, fry 20 to 80, juveniles, 35 to 130; steelhead--adults, 170 to 500, spawning, 130 to 400, fry, 20 to 70, juveniles, 70 to 350; pink spawning, 70 to 300; chum spawning in Squire Creek and Jim Creek, 70 to 450. Water temperatures measured in late summer at all sites ranged between 14.5 to 17.5 C. (Lantz-PTT)

Water-Resources Investigations Report↗
USGS1997

Distribution of fish, benthic invertebrate, and algal communities in relation to physical and chemical conditions, Yakima River basin, Washington, 1990

Biological investigations were conducted in the Yakima River Basin, Washington, in conjunction with a pilot study for the U.S. Geological Survey's National Water-Quality Assessment Program. Ecological surveys were conducted at 25 sites in 1990 to (1) assess water-quality conditions based on fish, benthic invertebrate, and algal communities; (2) determine the hydrologic, habitat, and chemical factors that affect the distributions of these organisms; and (3) relate physical and chemical conditions to water quality. Results of these investigations showed that land uses and other associated human activities influenced the biological characteristics of streams and rivers and overall water-quality conditions. Fish communities of headwater streams in the Cascades and Eastern Cascades ecoregions of the Yakima River Basin were primarily composed of salmonids and sculpins, with cyprinids dominating in the rest of the basin. The most common of the 33 fish taxa collected were speckled dace, rainbow trout, and Paiute sculpin. The highest number of taxa (193) was found among the inverte- brates. Insects, particularly sensitive forms such as mayflies, stoneflies, and caddisflies (EPT--Ephemeroptera, Plecoptera, and Trichoptera fauna), formed the majority of the invertebrate communities of the Cascades and Eastern Cascades ecoregions. Diatoms dominated algal communities throughout the basin; 134 algal taxa were found on submerged rocks, but other stream microhabitats were not sampled as part of the study. Sensitive red algae and diatoms were predominant in the Cascades and Eastern Cascades ecoregions, whereas the abundance of eutrophic diatoms and green algae was large in the Columbia Basin ecoregion of the Yakima River Basin. Ordination of physical, chemical, and biological site characteristics indicated that elevation was the dominant factor accounting for the distribution of biota in the Yakima River Basin; agricultural intensity and stream size were of secondary importance. Ordination identified three site groups and three community types. Site groups consisted of (1) small streams of the Cascades and Eastern Cascades ecoregions, (2) small streams of the Columbia Basin ecoregions, and (3) large rivers of the Cascades and Columbia Basin ecoregions. The small streams of the Columbia Basin could be further subdivided into two groups--one where agricultural intensity was low and one where agricultural intensity was moderate to high. Dividing the basin into these three groups removed much of the influence of elevation and facilitated the analysis of land-use effects. Community types identified by ordination were (1) high elevation, cold-water communities associated with low agricultural intensity; (2) lower elevation, warm-water communities associated with low agricultural intensity, and (3) lower elevation, warm-water communities associated with moderate to high agricultural intensity. Multimetric community condition indices indicated that sites in the Cascades and Eastern Cascades site group were largely unimpaired. In contrast, all but two sites in the Columbia Basin site group were impaired, some severely. Agriculture (nutrients and pesticides) was the primary factor responsible for this impairment, and all impaired sites were characterized by multiple indicators of impairment. Three sites (Granger Drain, Moxee Drain, and Spring Creek) had high levels of impairment. Sites in the large-river site group were moderately to severely impaired downstream from the city of Yakima. High levels of impairment at large-river sites corresponded with high levels of pesticides in fish tissues and the occurrence of external anomalies.

Washington↗
USGS1998

Trace elements and organic chemicals in stream-bottom sediments and fish tissues, Red River of the North basin, Minnesota, North Dakota, and South Dakota, 1992-95

Stream-bottom sediment and fish-tissue samples from the Red River of the North Basin, were analyzed for a large suite of chemical elements and organic chemicals. Cadmium, lead, and mercury were widespread in sediments, at concentrations not indicative of acute contamination. Mercury, the element of greatest health concern in the region, was detected at low concentrations in 38 of 43 sediment samples (<0.02-0.13 micrograms per gram) and all of eleven fish-liver samples (0.03-0.6 micrograms per gram dry weight, or 0.0066-0.13 micrograms per gram wet weight). Concentrations of many elements appeared to be controlled by mineral rather than anthropogenic sources. DDT and its metabolites were the most frequently detected synthetic organochlorines: p , p '-DDE was detected in 9 of 38 sediment samples (concentration range: <1-16 nanograms per gram) and also frequently in whole-fish samples. Total DDT (the sum of DDT and its metabolites) concentrations ranged from <5 to 217 nanograms per gram, and at least one component of total DDT was detected in 19 of 23 fish samples. Concentrations of DDT and its metabolites in stream sediments were significantly higher in the intensively cropped Red River Valley Lake Plain, compared to upland areas, probably because of greater historical DDT usage in the lake plain. Several polycyclic aromatic hydrocarbons were detected in stream-bottom sediments. Although the potentially toxic chemicals measured in this study were at low levels, relative to more contaminated areas of the Nation, maximum concentrations of some chemicals are of concern because of their possible effects on aquatic biota and human health.

Minnesota, North Dakota, South Dakota↗
USGS1998

Dioxins and furans in bed sediment and fish tissue of the Willamette Basin, Oregon, 1992-95

Polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/F) are related compounds that are of interest primarily because of their potential toxicity. They are considered carcinogens and have been implicated as hormone disrupters. An occurrence and distribution study of these compounds in the Willamette Basin, Oregon, was done by the U.S. Geological Survey in 1992- 1995. Bed sediment samples were collected at 22 sites, and fish tissue samples were collected from 8 sites. Samples were analyzed for 10 tetra- through octa- congener class totals and for 17 individual 2,3,7,8-substituted congeners. PCDD/Fs were found in bed sediment and fish tissue throughout the basin, including samples from the most remote forested sites. PCDD/F concentrations in bed sediment at most sites in agricultural and forested areas were similar to those at reference sites worldwide and are probably background concentrations due to atmospheric deposition. The highest concentrations in bed sediment were found at sites where industrial or urban inputs were likely. Potential toxicity at these sites (as measured by toxicity equivalents concentration) was high enough to be associated with increased risk to sensitive wildlife. From 30-60 percent of the toxicity equivalents concentration in bed sediment was due to hepta- and octa- congeners. The most toxic congener, 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD), was detected at only 6 of 22 sites. Compared to bed sediment from the same site, fish tissue usually had a lower total PCDD/F concentration, but contained a higher proportion of the most toxic congeners, such as 2,3,7,8-TCDD and 2,3,7,8-tetrachlorodibenzofuran. Because of these differences, toxicity equivalents concentrations in fish were higher than those in bed sediment from the same site at half of the sites where both media were analyzed.

Oregon↗
USGS1999

Relation of fish community composition to environmental and land use factors in part of the Upper Mississippi River Basin, 1995-97

Fish communities in the Upper Mississippi River Basin have been affected by changing environmental and land-use factors. Fish communities in small streams in agricultural and urban basins were compared to the fish community in a relatively undisturbed forested basin. In small streams, nutrient inputs from fertilizer, habitat modification from channelization, hydrologic modification from dams and tile drains, and increased water temperatures from loss of riparian shading have contributed to producing a change in fish community composition. In the large rivers, some of the changes that have occurred from sites upstream to downstream of the Twin Cities metropolitan area are primarily caused by the environmental effects of dams constructed as part of the lock and dam commercial navigation system. Although some of the differences upstream and downstream of the Twin Cities metropolitan area are due to zoogeographic variability, the major changes in the downstream community are shifts to more lentic species, species with higher thermal tolerance, and more planktivorous species. These changes are an extension of the changes observed in the small streams due to increased nutrients, increased water temperatures, and habitat alteration.

Minnesota↗
USGS1989

Spiral swimming behavior due to cranial and vertebral lesions associated with Cytophaga psychrophila infections in salmonid fishes

C. psychrophila infections of the cranium and anterior vertebrae in salmonid fishes were associated with ataxia, spiral swimming along the axis of the fish, and death. The syndrome was observed in 2-10% of underyearling coho salmon Oncorhynchus kisutch, rainbow trout Salmo gairdneri, and steelhead trout S. gairdneri at several private, state, and federal hatcheries in Washington and Oregon, USA, between 1963 and 1987. Affected fish did not recover and ultimately died. Histological examination consistently revealed subacute to chronic periostitis, osteitis, meningitis, and ganglioneuritis. Inflammation and periosteal proliferation of the anterior vertebrae at the junction of the vertebral column with the cranium with extension into the cranial case was a consistent feature. The adjacent nervous tissue, particularly the medulla, was often compressed by the proliferative lesion, and this may have caused the ataxia. Though bacteria were seldom observed in these lesions. C. psychrophila was isolated in culture from the cranial cavity of all affected fish that were tested. Epidemiological observations suggested that this bacterium is the causative agent because the spiral swimming behaviour and lesions were observed only in populations that had recovered from acute C. psychrophila infections.

Diseases of Aquatic Organisms↗
USGS2014

Estimating movement and survival rates of a small saltwater fish using autonomous antenna receiver arrays and passive integrated transponder tags

We evaluated the performance of small (12.5 mm long) passive integrated transponder (PIT) tags and custom detection antennas for obtaining fine-scale movement and demographic data of mummichog Fundulus heteroclitus in a salt marsh creek. Apparent survival and detection probability were estimated using a Cormack Jolly Seber (CJS) model fitted to detection data collected by an array of 3 vertical antennas from November 2010 to March 2011 and by a single horizontal antenna from April to August 2011. Movement of mummichogs was monitored during the period when the array of vertical antennas was used. Antenna performance was examined in situ using tags placed in wooden dowels (drones) and in live mummichogs. Of the 44 tagged fish, 42 were resighted over the 9 mo monitoring period. The in situ detection probabilities of the drone and live mummichogs were high (~80-100%) when the ambient water depth was less than ~0.8 m. Upstream and downstream movement of mummichogs was related to hourly water depth and direction of tidal current in a way that maximized time periods over which mummichogs utilized the intertidal vegetated marsh. Apparent survival was lower during periods of colder water temperatures in December 2010 and early January 2011 (median estimate of daily apparent survival = 0.979) than during other periods of the study (median estimate of daily apparent survival = 0.992). During late fall and winter, temperature had a positive effect on the CJS detection probability of a tagged mummichog, likely due to greater fish activity over warmer periods. During the spring and summer, this pattern reversed possibly due to mummichogs having reduced activity during the hottest periods. This study demonstrates the utility of PIT tags and continuously operating autonomous detection systems for tracking fish at fine temporal scales, and improving estimates of demographic parameters in salt marsh creeks that are difficult or impractical to sample with active fishing gear.

Marine Ecology Progress Series↗