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At least 1,081 records · Page 60Linked to original sources
USGS2016

Aquatic biological communities and associated habitats at selected sites in the Big Wood River Watershed, south-central Idaho, 2014

Assessments of streamflow (discharge) parameters, water quality, physical habitat, and biological communities were completed between May and September 2014 as part of a monitoring program in the Big Wood River watershed of south-central Idaho. The sampling was conducted by the U.S. Geological Survey in cooperation with Blaine County, Trout Unlimited, the Nature Conservancy, and the Wood River Land Trust to help identify the status of aquatic resources at selected locations in the watershed. Information in this report provides a basis with which to evaluate and monitor the long-term health of the Big Wood River and its major tributaries. Sampling sites were co-located with existing U.S. Geological Survey streamgaging stations: three on the main stem Big Wood River and four on the North Fork Big Wood River (North Fork), Warm Springs Creek (Warm Sp), Trail Creek (Trail Ck), and East Fork Big Wood River (East Fork) tributaries. The analytical results and quality-assurance information for water quality, physical habitat, and biological community samples collected at study sites during 2 weeks in September 2014 are summarized. Water-quality data include concentrations of major nutrients, suspended sediment, dissolved oxygen, and fecal-coliform bacteria. To assess the potential effects of nutrient enrichment on algal growth, concentrations of periphyton biomass (chlorophyll- a and ash free dry weight) in riffle habitats were determined at each site. Physical habitat parameters include stream channel morphology, habitat volume, instream structure, substrate composition, and riparian vegetative cover. Biological data include taxa richness, abundance, and stream-health indicator metrics for macroinvertebrate and fish communities. Statistical summaries of the water-quality, habitat, and biological data are provided along with discussion of how these findings relate to the health of aquatic resources in the Big Wood River watershed. Seasonal discharge patterns using statistical summaries of daily discharge from selected sites are reported for water years 2012–15. Results showed that annual average daily mean discharge increased from the Big Wood River near Ketchum, ID (BW Ketchum) downstream to the Big Wood River at Hailey, ID (BW Hailey), but decreased by nearly 50 percent from BW Hailey downstream to Big Wood River at Stanton Crossing near Bellevue, ID (BW Stanton). Annual variability in daily mean discharge among main-stem sites was highest at BW Stanton, suggesting that this part of the river may be subject to some level of flow alteration. Hydrologic alterations resulting in flow reduction can contribute to higher water temperature, especially during the summer months when conditions are often most stressful to fish and other stream organisms. Daily water temperature and water temperature trends from June to September 2014 are reported for select tributary and main-stem sites on the Big Wood River and can be used to assess the potential for biological impairment based on aquatic life temperature criteria for cold-water streams. The State of Idaho maximum temperature criteria for protection of cold-water aquatic life of 22 °C was exceeded at Warm Sp and BW Stanton during summer 2014, but at none of the other main-stem or tributary sites. The 13 °C critical temperature criterion for salmonid spawning was exceeded in early July 2014 at BW Ketchum and BW Hailey near the end of the rainbow trout critical spawning and rearing period. Temperature exceedances were most frequent at BW Stanton, where exceedances for rainbow trout and brown trout occurred from May through early July 2014 during most of the critical spawning and rearing period. Water quality and habitat availability did not seem to be limiting for fish or other aquatic organisms at most sites in the Big Wood River watershed. Water quality assessments in September 2014 determined no exceedances of total maximum daily load target levels. The availability and quality of habitat was limited at BW Stanton, where shallow-water habitat conditions prevailed. Macroinvertebrate community diversity was high at all sites except for BW Stanton, where low community diversity was attributed to low species richness and high abundances of a few tolerant taxa. Presence of low species diversity and high macroinvertebrate tolerance values at BW Stanton indicates that benthic community condition and stream health were reduced at that location. Fish surveys done in September 2014 did not indicate any significant reductions in native fish communities in the Big Wood River or its tributaries. Native rainbow trout ( Oncorhynchus mykiss ) and Wood River sculpin ( Cottus leiopomus ) were the dominant fish species in the drainage and were found at all tributary and main-stem sites. Non-native brown ( Salmo trutta ) and brook trout ( Salvelinus fontinalis ) were limited to lower drainage sites on the Big Wood River (BW Hailey and BW Stanton), and occurred in relatively low numbers.

Idaho↗
USGS2017

Suspended sediment, turbidity, and stream water temperature in the Sauk River Basin, western Washington, water years 2012-16

The Sauk River is a federally designated Wild and Scenic River that drains a relatively undisturbed landscape along the western slope of the North Cascade Mountain Range, Washington, which includes the glaciated volcano, Glacier Peak. Naturally high sediment loads characteristic of basins draining volcanoes like Glacier Peak make the Sauk River a dominant contributor of sediment to the downstream main stem river, the Skagit River. Additionally, the Sauk River serves as important spawning and rearing habitat for several salmonid species in the greater Skagit River system. Because of the importance of sediment to morphology, flow-conveyance, and ecosystem condition, there is interest in understanding the magnitude and timing of suspended sediment and turbidity from the Sauk River system and its principal tributaries, the White Chuck and Suiattle Rivers, to the Skagit River. Suspended-sediment measurements, turbidity data, and water temperature data were collected at two U.S. Geological Survey streamgages in the upper and middle reaches of the Sauk River over a 4-year period extending from October 2011 to September 2015, and at a downstream location in the lower river for a 5-year period extending from October 2011 to September 2016. Over the collective 5-year study period, mean annual suspended-sediment loads at the three streamgages on the upper, middle, and lower Sauk River streamgages were 94,200 metric tons (t), 203,000 t, and 940,000 t streamgages, respectively. Fine (smaller than 0.0625 millimeter) total suspended-sediment load averaged 49 percent at the upper Sauk River streamgage, 42 percent at the middle Sauk River streamgage, and 34 percent at the lower Sauk River streamgage.

Washington↗
USGS2019

Arsenic, antimony, mercury, and water temperature in streams near Stibnite mining area, central Idaho, 2011–17

Mineralization and historical mining of stibnite (antimony sulfide), tungsten, gold, silver, and mercury in the headwaters of the East Fork of the South Fork Salmon River (EFSFSR) near the former town of Stibnite in central Idaho resulted in water-quality impairments related to mercury, antimony, and arsenic. Additionally, mining-related disturbances and wildfires have resulted in a lack of riparian shade in some areas, likely impacting water temperatures. In 2011, the U.S. Geological Survey, in cooperation with Midas Gold Corporation and the Idaho Department of Lands, began a study to characterize the spatial and temporal occurrence of trace metals to the EFSFSR. Five sites on the EFSFSR and its tributaries (Meadow and Sugar Creeks) were sampled about six times annually during 2011–17, during a range of streamflow conditions, for a total of 36–40 samples per location. Continuous water temperature, specific conductance, and streamflow also were measured at each site. The purpose of this report is to update previously reported information related to arsenic, antimony, mercury, and water temperature. Concentrations of dissolved arsenic and antimony generally increased from upstream to downstream in the EFSFSR. At the upstream site, upstream of the Meadow Creek confluence, dissolved arsenic and antimony concentrations averaged 8.86 and 0.93 micrograms per liter (μg/L), respectively. Downstream, upstream from the Sugar Creek confluence, average dissolved concentrations increased to 56.5 and 27.9 μg/L, respectively. All samples from the downstream EFSFSR site exceeded the human-health based criterion for both dissolved arsenic (10 µg/L) and dissolved antimony (5.6 µg/L). The chronic aquatic life criterion for dissolved arsenic (150 μg/L) was not exceeded (the maximum sample concentration was 108 μg/L), and aquatic life criteria for antimony have not been established. The highest concentrations of both dissolved arsenic and dissolved antimony occurred during low-flow periods (July–March), suggesting the constituents are present in groundwater. In contrast, total mercury concentrations were highest during high-flow periods (April–June) and were particulate-associated, suggesting that mercury is present in surface materials. At Sugar Creek, where the highest total mercury concentrations were measured, 97 percent of samples exceeded the chronic aquatic life criterion (0.012 μg/L) and 11 percent exceeded the acute criterion (2.1 μg/L). At all sites, summertime water temperatures frequently exceeded criteria related to salmonid spawning. Surrogate models previously developed to estimate continuous concentrations of arsenic, antimony, and mercury were reevaluated and updated, and the importance of explanatory variables on constituent concentrations is discussed. Results from this study can help guide future remediation locations and strategies, and provide a baseline against which future changes can be measured.

Idaho↗
USGS2022

Estimating stream temperature in the Willamette River Basin, northwestern Oregon—A regression-based approach

The alteration of thermal regimes, including increased temperatures and shifts in seasonality, is a key challenge to the health and survival of federally protected cold-water salmonids in streams of the Willamette River basin in northwestern Oregon. To better support threatened fish species, the U.S. Army Corps of Engineers (USACE) and other water managers seek to improve the thermal regime in the Willamette River and key tributaries downstream of USACE dams by utilizing strategically timed flow releases from USACE dams. To inform flow management decisions, regression relations were developed for 12 Willamette River basin locations below USACE dams relating stream temperature with streamflow and air temperature utilizing publicly available datasets spanning 2000–18. The resulting relations provide simple tools to investigate stream temperature responses to changes in streamflow and climatic conditions in the Willamette River system. Regression relations on the Willamette River and key tributaries show that, at locations sufficiently distant from the direct temperature influence of upstream dam releases, air temperature and streamflow are reasonable proxies to predict the 7-day average of the daily mean (7dADMean) and 7-day average of the daily maximum (7dADMax) water temperature with errors generally ≤1 degrees Celsius (°C). To account for seasonal variations in the relation between air temperature, streamflow, and stream temperature, a transition-smoothed, seasonal regression approach was used. Stream temperature is inversely correlated with streamflow in all seasons except “winter” (January–March), when it is relatively independent. Stream temperature is positively correlated with air temperature in all seasons, but the slope decreases at very low or very high air temperatures. Generally, fit is best for seasonal models “winter” (January–March), “spring” (April–May), “summer” (June–August), and “early autumn” (September–October). Error in “autumn” (November–December) is larger, probably due to variation in the onset timing of winter storms. Simulated results from a climatological analysis of predicted stream temperature suggest that, excluding extremes and accounting for some seasonal variability, the 7dADMean and 7dADMax stream temperature sensitivity to air temperature and streamflow varies by location on the river. To investigate the potential range of stream temperature variability based on historical air temperature and streamflow conditions, stream temperature predictions were calculated using synthetic time series comprised of daily temperature values representing the 0.10, 0.33, 0.50, 0.67, and 0.90 quantile of air temperature and streamflow from 1954 (the year meaningful streamflow augmentation began) to 2018. Results show that from a “very hot” (0.90 quantile) and “very dry” (0.10 quantile) year to a “very cool” (0.10 quantile) and “very wet” (0.90; all quantiles from 1954 to 2018) year, the stream temperature sensitivity to air temperature and streamflow is about 3 °C at Harrisburg (river mile 161.0) and increases to about 5 °C at Keizer (river mile 82.2). While the number of days exceeding regulatory criteria are fewer in cooler, wetter years than in warmer, dryer years, the models suggest that the Willamette River will likely continue to exceed the State of Oregon maximum water-temperature criterion of 18 °C for sustained periods from late spring to early autumn and that the flow management practices evaluated in this study, while effective at influencing stream temperature, likely cannot prevent many or all such exceedances. As modeled for 2018, a representative very hot year with normal to below-normal streamflow, stream temperature sensitivity to changes in streamflow of ±100 to ±1000 cubic feet per second produced mean monthly temperature changes from 0.0 to 1.4 °C at Keizer, Albany, and Harrisburg during summer. For a specified change in flow, temperature sensitivity is greater at upstream locations where streamflow is less than that at downstream locations because the change in streamflow is a greater percentage of total streamflow at upstream locations. Similarly, temperature response to a set change in flow is greater in the summer and early autumn low-flow season than in spring when flows are higher. The regression models developed in this study thus indicate that flow management is likely to have a greater effect on stream temperature at upstream locations (such as Harrisburg or Albany) and during the low-flow season than at downstream locations (such as Keizer) or during periods of higher streamflow.

Oregon↗
USGS2021

Streambed scour of salmon (Oncorhynchus spp.) redds in the Sauk River, Northwestern Washington

The autumn and winter flood season of western Washington coincides with the incubation period of many Pacific salmon ( Onchorhynchus spp.) populations. During this period, salmon embryos incubating within gravel nests called “redds” are vulnerable to mobilization of surrounding sediment during floods. As overlying sediment is transported downstream, the vertical position of the streambed can be lowered, a process termed streambed scour; thus developing salmon embryos may be destroyed resulting in decreasing egg-to-fry survival rates. The Sauk River, which drains a 1,900 km 2 (733.5 mi 2 ) area of the central Cascade Range of Washington State, provides spawning and rearing habitat for several species of Pacific salmon including Chinook salmon ( O. tshawytscha ), which were listed as threatened under the Endangered Species Act (ESA) in 1999. In order to assess the hydrologic conditions when streambed scour and concomitant geomorphic changes occur, accelerometer scour monitors (ASMs), which record the time when streambed scour lowers the streambed to the level of salmon egg pockets, were deployed in two geomorphically different reaches of the Sauk River to monitor scour during water year 2018. Nineteen ASMs were deployed in an upstream reach, which was largely confined by valley walls with vegetated, stable banks and low channel-migration rates near the confluence of the Sauk and White Chuck Rivers. Twelve additional ASMs were deployed in a downstream reach within an unconfined valley with unvegetated, unstable banks and high channel-migration rates between the town of Darrington and the confluence of the Sauk and Suiattle Rivers. During the ASM deployment, discharge measured at the U.S. Geological Survey (USGS) streamgage Sauk River above White Chuck River, near Darrington, Washington (12186000), peaked at 479 m 3 /s (16,900 ft 3 /s) with an estimated 0.18 probability of annual exceedance (5.7-year recurrence interval). During the flood season, large-scale geomorphic changes, including channel migration and bar deposition, were measured at the downstream reach, but only minimal geomorphic changes were measured at the upstream reach. ASMs deployed at the downstream reach were not recovered after the flood season and total scour depth was presumed to have exceeded ASM anchor depth. At the upstream reach, 7 of the 19 deployed ASMs were recovered after the flood season and all recovered ASMs recorded scour at discharges that equaled or exceeded 204 m 3 /s (7,210 ft 3 /s). The remaining 12 ASMs deployed at the upstream reach were not recovered and total scour depth was presumed to have exceeded ASM anchor depth. Collectively, this analysis enhances the ability of fisheries managers to forecast egg-to-fry survival rates of salmonids by determining the hydrologic conditions at which scour at the level of salmon redds initiates.

Washington↗
USGS2022

Geohydrology and water quality of the northern and central parts of the Tug Hill glacial aquifer, Jefferson and Oswego Counties, north-central New York

The northern and central parts of the Tug Hill glacial aquifer consist of a 29-mile-long, crescent-shaped, mixture of glaciofluvial, glaciolacustrine, and recent alluvial deposits of predominantly sand and gravel on the western side of the Tug Hill Plateau in Jefferson and Oswego Counties in north-central New York. Approximately 11,400 people are supplied by groundwater that is withdrawn from municipal and nonmunicipal wells in the northern and central parts of the aquifer. In addition, many farms, several industries, and a large New York State fish hatchery also rely on the water from the aquifer. In the early 2000s, anticipated developmental pressures from potential new industries (including a proposed water-bottling plant in the central part of the Tug Hill glacial aquifer) and expansion of the Fort Drum military base north of Watertown (with the projected increase in population extending into the northern part of the aquifer) prompted the Tug Hill Commission, local municipal officials, and representatives from the New York State Department of Environmental Conservation to initiate a geohydrologic study with the U.S. Geological Survey. The information from this study is intended to help the state, counties, and local communities make sound policy decisions about their use of this large groundwater resource. The northern part of the Tug Hill glacial aquifer is a combination of glaciofluvial outwash and alluvial sand and gravel in the Sandy Creek Valley northeast of Adams, New York, and mostly glaciolacustrine beach and deltaic sand or sand and gravel north and south of the village of Adams. The southern and eastern areas of the central part of the aquifer are composed mostly of glaciofluvial sediments such as kames, kame moraines, and kame terraces, whereas most of the western areas of the central part are composed mostly of glaciolacustrine sediments such as deltaic sand and beach sand and gravel. The northern and central parts of the aquifer are unconfined. Recharge to the northern and central parts of the aquifer is from three main sources: (1) precipitation that falls directly onto the aquifer; (2) unchannelized runoff (overland flow) and groundwater from till and bedrock in the Tug Hill Plateau that seeps into the eastern side of the aquifer; and (3) streams that drain the Tug Hill Plateau and flow across and lose water to the aquifer. Groundwater discharges to springs, seeps, headwaters of streams, and wetlands in the middle area of the central part of the aquifer and along the entire western boundary of the northern and central parts of the aquifer; pumping wells; artificial ditches; and deeply incised streams in the northern and central parts of the aquifer. The groundwater discharge to such streams is critical in supporting the salmonid fishery in the central part of the aquifer. Groundwater levels were measured on July 17, 2014, at 22 wells throughout the northern and central parts of the aquifer. Water-table contours were drawn on the basis of the measured July 2014 water levels, historical water-level data, and surface-water levels where surface water in the channels was expected to be hydraulically connected to the groundwater system. The water table generally slopes from east to west throughout the northern and central parts of the aquifer; this slope also indicates that the direction of groundwater flow is generally from east to west. Water-quality samples were collected from 23 stream sites during base-flow conditions, and groundwater-quality and other types of environmental samples were collected from 20 wells in the northern and central parts of the Tug Hill glacial aquifer. The results of the sampling indicate that surface water and groundwater are generally of good quality. Comparison of the median concentration values of major ions in groundwater samples indicated that hardness in the northern part of the aquifer was about twice as great, and concentrations of calcium and sodium were more than three times as great, as in the central part of the aquifer. As was the case with surface water, the much greater median concentrations in groundwater of calcium, hardness, and alkalinity in the northern part of the aquifer are due to the dissolution of limestone that underlies most of that area and to the high-carbonate content of the clasts in the sand and gravel. There was little to no difference among the median values for bromide, fluoride, silica, and iron in the two parts of the aquifer. Concentrations of most other major ions were slightly greater in the northern part than in the central part of the Tug Hill glacial aquifer, except for magnesium, whose concentration was greater in the central part. Median concentrations of nutrients were generally greatest in surface water and groundwater in the northern part of the aquifer.

New York↗
USGS2022

Longitudinal water-temperature profiles in Mill Creek, Mason County, Washington

In streams supporting Pacific salmon ( Oncorhynchus spp.) within the southern Puget Lowland, high water temperatures during late summer are a primary water-quality concern. The metabolic rates of fish and other ectothermic (in other words, cold-blooded) species are regulated by water temperature; salmon and other cold-water fish have specific thermal tolerances outside of which they are susceptible to infection, disease, increased predation, and decreased reproductive success. Mill and Gosnell Creeks, which collectively drain a 30-square mile area of the Puget Lowland in Mason County, Washington, support several species of anadromous salmonids. Whereas previous studies documented relatively cool water temperatures in Gosnell Creek, which drains the watershed upstream from Lake Isabella, water temperatures in Mill Creek, which heads at the outlet of Lake Isabella, regularly exceed thermal tolerances for cold-water fish. The occurrence and distribution of cold-water anomalies in less-than-ambient water temperatures in Mill Creek, however, have not been assessed. In this report, we present spatially and temporally continuous measurements of near-streambed water temperature measured using fiber-optic distributed temperature sensing for three reaches of Mill Creek during August–September 2020 when the water temperatures of streams in western Washington were near their annual maximum. Water temperature was collected every hour and averaged spatially over 1.015-meter sections of the fiber-optic cable deployed at the streambed of Mill Creek. The lengths of the fiber-optic cables deployed in Reaches A, B, and C were 883, 270, and 1,014 meters, respectively. Daily maximum water temperature and daily temperature variability, as measured by standard deviation of water temperature during the deployment, progressively decreased downstream as distance from Lake Isabella increased. However, no abrupt decreases in daily maximum or standard deviation of water temperature were detected in longitudinal temperature profiles of any of the three reaches. Collectively, these results suggest that warm water discharged from Lake Isabella was progressively buffered downstream as it equilibrated with downstream heat fluxes mediated by physical processes including riparian shading and diffuse groundwater input. Although parts of the surveyed reaches associated with deep pools were cooler than other locations, no large (less than 2 °C) water-temperature anomalies characteristic of discrete sources of cold groundwater or surface-water inputs were measured in any of the three surveyed reaches.

Washington↗
USGS2023

Assessing the presence of current-use pesticides in mid-elevation Sierra Nevada streams using passive samplers, California, 2018–19

Passive sampler devices were deployed in six northern California streams five times between November 2018 and December 2019 to measure the presence or absence of current-use pesticides in surface water. In the targeted areas, there are reported pesticide uses for agriculture, commercial forestry, and rights of way maintenance along with unreported pesticide use at private residences and cannabis grow sites. The sites sampled in this study were not previously monitored for current-use pesticides. Streams in the Sierra Nevada foothills of northern California are important habitats for many sensitive species including salmonids, but the logistics of sampling these areas can be difficult using traditional water-quality sampling techniques, especially when sampling watersheds where contaminant transport is episodic. Chemcatcher passive sampling devices and silicone bands were deployed in these areas to concentrate pesticides for days to weeks at a time. The U.S. Geological Survey, in cooperation with the Central Valley Regional Water Quality Control Board, was responsible for developing passive sampler field deployment and laboratory analytical methods for current-use pesticides, providing pesticide measurements from streams in the study region, and determining how well passive samplers detect pesticides in these environments. Six sites were monitored during the study, and passive sampler extracts were analyzed for a total 155 current-use pesticides in this study. A total of 19 out of the 155 pesticides including 9 insecticides, 5 fungicides, and 5 herbicides were detected in extracts from passive samplers. The most frequently detected pesticides were the herbicides hexazinone and dithiopyr, the insecticides bifenthrin and methoxyfenozide, and the fungicide azoxystrobin.

California↗
USGS2023

Sediment transport in two tributaries to the San Joaquin River immediately below Friant Dam—Cottonwood Creek and Little Dry Creek, California

Two tributaries to the greater San Joaquin River watershed, Cottonwood and Little Dry Creeks, in California’s Central Valley, were assessed for sediment and streamflow dynamics between October 1, 2011, and September 30, 2019. The two systems deliver sediment to the San Joaquin River below Friant Dam, California. Dams create downstream discontinuities in streamflow and sediment transport and therefore influence fish habitat and sediment dynamics. Because these two creeks are directly downriver from Friant Dam, they become the most upstream source of sediment to the San Joaquin River below Friant Dam. The quality and quantity of spawning habitat for fish in the gravel-bedded reach of the San Joaquin River relies on a range of bed material particle size suitable for redd structure. The effects of coarse-sand to fine-gravel supply on salmonid habitat depends primarily on the size of the sediment and the timing of its addition from tributaries to the San Joaquin River; thus, understanding the timing, quantity, and size of sediment supplied from these two tributaries is critical to the management of ecological and biological sustainability. Streamflow from Cottonwood and Little Dry Creeks, along with streamflow from the San Joaquin River below Friant Dam, were compared to continuously measured water-surface elevations to quantify the timing and direction of streamflow. Suspended-sediment samples were collected with multiple automatic samplers and analyzed for concentration and grain-size distribution. Measured suspended-sediment concentrations and streamflows were used to develop sediment rating curves and compute continuous estimates of suspended-sediment load for each tributary. Satellite imagery was used to qualify spatial and temporal dynamics through the lower watersheds and support more quantitative sediment-load estimates. Computed annual sediment loads ranged from 1.32x10 1 to 2.68x10 4 metric tons for Little Dry Creek and 9.82 to 1.98x10 3 metric tons for Cottonwood Creek. Sediment loads computed during the study period for both watersheds show that annual loads were highest during water year 2017 (October 1, 2016, to September 30, 2017). Sediment transport primarily occurred between the months of January and March. In both tributaries, grain-size distributions of suspended sediment were predominantly coarse-sized sand and were finer than the remnant bed material. Both creeks demonstrate backwater effects from the San Joaquin River, but the more tortuous stream channel and historical mining pits within Little Dry Creek provide more capacity for sediment storage compared to the less complex stream network of Cottonwood Creek. Because loads were computed based on upstream streamgages and not at the confluence of each tributary to the San Joaquin River, annual load estimates do not represent direct flux into the San Joaquin River; instead, these results indicated that in Little Dry Creek, particularly, the lowest portion of the watershed stores sediment before it reaches the San Joaquin River.

California↗
USGS2024

Extent and duration of cold-water areas associated with side channels and tributaries of the lower Yakima River, Washington, September 2018–20

Previous work on the lower Yakima River, Washington (downstream from Union Gap), has identified several cold-water areas that could be thermal refuges for migrating salmonids. These cold-water areas are characterized by small tributaries that are typically cooler than the main-stem river during summer months (June–August). Twenty-seven temperature sensors were deployed along the lower 90 miles of the Yakima River at 7 locations where cold water had been previously observed. Deployments lasted from 1 to 2 years from September 2018 to September 2020 to document the extent and duration of these cold-water areas. Cold-water areas included the mouths of tributaries, alongside channels, and alcoves. Throughout summer months, main-stem river temperatures were warm, averaging about 92 days, when maximum daily temperatures exceeded 21 degrees Celsius (°C). The relationship between temperatures in the lower Yakima River and its tributaries varied seasonally; tributary water temperatures were 2–10 °C cooler than the main-stem river during summer months but 6–10 °C warmer than main-stem temperatures during winter months. The cooling effect of tributary inputs reduced downstream temperatures in the main stem by an average of 2–4 °C up to 175 feet downstream from tributary mouths. Side channel locations showed evidence of cooling, most likely from subsurface groundwater seeps, but the magnitude of cooling was less evident compared to tributaries. This study provides new information on spatial and temporal dynamics of cold-water areas on the lower Yakima River, which might provide cold-water habitat for migrating fishes in the future.

Washington↗
USGS2024

U.S. Geological Survey Tunison Laboratory of Aquatic Science research to rehabilitate native prey fish of the Lake Ontario fish community—Coregonine fishes

Restoration of native coregonines to Lake Ontario of the Laurentian Great Lakes will improve the diversity of forage for salmonid predators and ecological function in the lake, but efficacy of experimental releases for native species restoration must be evaluated. The Coregonine Research Program at the U.S. Geological Survey Tunison Laboratory of Aquatic Science encompassed a diverse array of research, with an emphasis on improved culture methods and field assessments of experimentally released juvenile coregonines. This research was carried out to support the Fish Community Objectives of the Lake Ontario Committee, is funded largely by the Great Lakes Restoration Initiative, and was done in collaboration with other laboratories and agencies, particularly, the U.S. Fish and Wildlife Service; New York State Department of Environmental Conservation; Ontario Ministry of Natural Resources and Forestry; and other U.S. Geological Survey laboratories. The Tunison Laboratory of Aquatic Science and partners have developed new and innovative hatchery techniques to raise cisco and bloater to life stages suitable for survival in Lake Ontario; assessed adult bloater survival in Lake Ontario; and evaluated survival, return rate, and reproduction of adult cisco in historic spawning locations in Lake Ontario embayments. Successes, challenges, and research needs are discussed.

Lake Ontario↗
USGS2025

Development of regression equations to estimate flow durations, low-flow frequencies, and mean flows at ungaged stream sites in Connecticut using data through water year 2022

To aid Federal and State regulatory agencies in the effective management of water resources, the U.S. Geological Survey, in cooperation with the Connecticut Department of Energy and Environmental Protection and the Connecticut Department of Transportation, updated flow statistics for 118 streamgages and developed 47 regression equations to estimate selected flow duration, low flow, and mean flow statistics for the entire State of Connecticut, for the following: 1-, 5-, 10-, 25-, 50-, 75-, 90-, 99-percent flow durations; 7-day, 10-year low-flow frequency and 30-day, 2-year low-flow frequency; and mean flow, spring mean flow, and harmonic mean flow. In addition, regression equations were developed for monthly and seasonal flow durations, ranging from 25 to 99 percent for aquatic biological processes of salmonid spawning (November), overwinter (December–February), clupeid spawning (May), resident spawning (June), and rearing and growth (July–October) periods, and for flow durations ranging from 1 to 99 percent for the habitat forming (March–April) period. Statistics were derived from daily mean streamflow data collected from streamgages with at least 10 years of data through water year 2022 in southern New England and eastern New York. Forty streamgages in Connecticut and adjacent areas of neighboring States were used in the regression analysis. Regression methods of weighted least squares and generalized least squares were used to derive the final coefficients and measures of uncertainty for the regression equations. The equations used to estimate selected streamflow statistics were developed by relating the flow statistics to different basin characteristics (physical, land cover, and climatic) at the 40 streamgages. Nine basin characteristics served as the explanatory variables in the statewide regression equations: drainage area, percentage of area with coarse-grained stratified deposits, stream density, mean basin slope, mean basin elevation, percentage of area with hydrologic soil group A, mean monthly precipitation for November, mean seasonal precipitation in the winter (December, January, and February), and mean annual temperature. The root mean square error of the 47 equations ranged from 7.9 to 121.9 percent, with an average of 27.9 percent. The equations estimate flows most accurately near the mean (50-percent flow duration), become less accurate for low flows, and are the least accurate for extreme low flows. The root mean square error for the 50-percent flow duration is 15.1 percent, with an average of 17.6 percent across the six periods. The extreme low flow statistics of 7-day, 10-year low-flow frequency, 99-percent flow duration, and 99-percent rearing and growth period flow durations have root mean square errors of 121.9, 105.1, and 121.9 percent, respectively. The adjusted coefficient of determination of the 47 equations ranged from 73.4 to 99.5 percent, with an average of 95.1 percent.

Connecticut↗
USGS1997

Fish communities of benchmark streams in agricultural areas of eastern Wisconsin

Fish communities were surveyed at 20 stream sites in agricultural areas in eastern Wisconsin in 1993 and 1995 as part of the National Water-Quality Assessment (NAWQA) Program. These streams, designated "benchmark streams," were selected for study because of their potential use as regional references for healthy streams in agricultural areas, based on aquatic communities, habitat, and water chemistry. The agricultural benchmark streams were selected from four physical settings, or relatively homogeneous units (RHU's), that differ in bedrock type, texture of surficial deposits, and land use. Additional data were collected along with the fish-community data, including measures of habitat, water chemistry, and population surveys of algae and benthic invertebrates. Of the 20 sites, 19 are classified as trout (salmonid) streams. Fish species that require cold or cool water were the most commonly collected. At least one species of trout was collected at 18 sites, and trout were the most abundant species at 13 sites. The species with the greatest collective abundance, and collected at 18 of the 20 sites, were mottled sculpin (Cottus bairdi), a coldwater species. The next most abundant species were brown trout (Salmo trutta), followed by brook trout (Salvelinusfontinalis), creek chub (Semotilus atromaculatus), and longnose dace (Rhinichthys cataractae). In all, 31 species of fish were collected. The number of species per stream ranged from 2 to 14, and the number of individuals collected ranged from 19 to 264. According to Index of Biotic Integrity (IBI) scores, 5 sites were rated excellent, 10 sites rated good, 4 rated fair, and 1 rated poor. The ratings of the five sites in the fair to poor range were low for various reasons. Two sites appeared to have more warmwater species than was ideal for a high-quality coldwater stream. One was sampled during high flow and the results may not be valid for periods of normal flow; the other may have been populated by migrating warmwater species. Two sites had insufficient deep-water habitat to support large numbers offish, especially top carnivores. Finally, one stream may be too cool to support enough warmwater species and too warm to support trout. In general, two methods of evaluating site habitat indicate that habitat is not a limiting factor for fish communities. However, two sites were rated as fair according to both habitat evaluation methods due to low base flow. Two sites rated below good according to one habitat evaluation method but rated good or excellent according to the other. Detrended correspondence analysis (DCA) of data for 17 sites showed three station groupings. These groupings fell along RHU divisions and each group was associated with one of three trout species. A species-richness gradient was evident on the station-ordination diagram. Intolerant species were associated with each grouping, a reflection of the generally high water quality at the sites. However, no significant differences were found between IBI scores or habitat indices among the site groupings. The DCA axis 1 and 2 scores correlated with average velocity and percent pool as well as RHU factors percent sandy surficial deposits, percent wetland, percent agriculture, and bedrock. Average velocity was highest at three sites which also had among the highest measured flow and largest drainage areas. Percent pool was generally lower at sites with smaller percentages of sandy surficial deposits, with one exception. The usefulness of ordination methods in conjunction with more traditional methods of defining biotic integrity (IB I) has been noted in previous studies. In this study, however, perhaps because of the relative homogeneity of the benchmark streams, the IBI did not correlate with the same kinds of factors as the DCA axis scores did.

Wisconsin↗
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↗
USGS1999

An assessment of stream habitat and nutrients in the Elwha River basin: implications for restoration

The Elwha River was once famous for its 10 runs of anadromous salmon which included chinook that reportedly exceeded 45 kilograms. These runs either ceased to exist or were significantly depleted after the construction of the Elwha (1912) and Glines Canyon (1927) Dams, which resulted in the blockage of more than 113 kilometers of mainstem river and tributary habitat. In 1992, in response to the loss of the salmon runs in the Elwha River Basin, President George Bush signed the Elwha River Ecosystem and Fisheries Restoration Act, which authorizes the Secretary of the Interior to remove both dams for ecosystem restoration. The objective of this U.S. Geological Survey (USGS) study was to begin describing baseline conditions for assessing changes that will result from restoration. The first step was to review available physical, chemical, and biological information on the Elwha River Basin. We found that most studies have focused on anadromous fish and habitat and that little information is available on water quality, habitat classification, geomorphic processes, and riparian and aquatic biological communities. There is also a lack of sufficient data on baseline conditions for assessing future changes if restoration occurs. The second component of this study was to collect water-quality and habitat data, filling information gaps. This information will permit a better understanding of the relation between physical habitat and nutrient conditions and changes that may result from salmon restoration. We collected data in the fall of 1997 and found that the concentrations of nitrogen and phosphorous were generally low, with most samples having concentrations below detection limits. Detectable concentrations of nitrogen were associated with sites in the lower reach of the Elwha River, whereas the few detections of phosphorus were at sites throughout the basin. Nutrient data indicate that the Elwha River and its tributaries are oligotrophic. Results of the stream classification indicated that most of the habitat that would be usable by salmon is found in the mainstem of the Elwha River due to natural gradient barriers at the lower end of most tributaries. Habitat is diverse in the mainstem due to large woody debris accumulations and the existence of secondary channels. We concluded that restoring salmon runs to the Elwha River system will affect the ecosystem profoundly. Decaying carcasses of migrating salmon will be the source of large quantities of nutrients to the Elwha River. The complex instream habitat of the mainstem will enhance cycling of these nutrients because carcasses will be retained long enough to be assimilated thereby increasing primary and secondary production, size of immature salmonids, and overall higher salmon recruitment.

Washington↗
USGS1969

Factors initiating phytoplankton blooms and resulting effects on dissolved oxygen in Duwamish River estuary, Seattle, Washington

Phytoplankton productivity, standing stock, and related environmental factors were studied during 1964-66 in the Duwamish River estuary, at Seattle, Wash., to ascertain the factors that affect phytoplankton growth in the estuary; a knowledge of these factors in turn permits the detection and evaluation of the influence that effluent nutrients have on phytoplankton production. The factors that control the concentration of dissolved oxygen were also evaluated because of the importance of dissolved oxygen to the salmonid populations that migrate through the estuary. Phytoplankton blooms, primarily of diatoms, occurred in the lower estuary during August 1965 and 1966. No bloom occurred during 1964, but the presence of oxygen-supersaturated surface water in August 1963 indicates that a bloom did occur then. Nutrients probably were not the primary factor controlling the timing of phytoplankton blooms. Ammonia ,and phosphate concentrations increased significantly downstream from the Municipality of Metropolitan Seattle's Renton Treatment Plant outfall after the plant began operation in June 1965, and concentrations of nitrogen and phosphorus were relatively high before operation of the Renton Treatment Plant and during nonbloom periods. The consistent coincidence of blooms with minimum fresh-water discharge and tidal exchange during August throughout the study period indicates that bloom timing probably was controlled mostly by hydrographic factors that determine retention time and stability of the surface-water layer. This control was demonstrated in part by a highly significant correlation of gross productivity with retention time (as indicated by fresh-water discharge) and vertical stability (as indicated by the difference between mean surface and mean bottom temperatures). The failure of a bloom to develop in 1964 is related to a minimum fresh-water discharge that was much greater than normal during that summer. Hydrographic factors are apparently important because, as shown by studies of other estuarine environments by other workers, phytoplankton production increases when the zone of vertical turbulent mixing is not markedly deeper than the compensation depth. Phytoplankton cells produced in the surface waters sink, thereby contributing oxidizable organic matter to the bottom saline-water wedge. The maximum BOD (biochemical oxygen demand) in this bottom wedge occurs in the same section of the estuary and ,at the same time as the maximum phytoplankton biomass (as indicated by chlorophyll a) and minimum DO (dissolved oxygen). Other sources of BOD occur in the estuary, and conditions of minimum discharge and tidal exchange assist in reducing DO. Nonetheless, the highly significant correlation of chlorophyll a with BOD throughout the summer indicates that respiration and decomposition of phytoplankton cells is dearly an important contributor of BOD. Increases in the biomass and resultant B0D of blooms because of increased effluent nutrients presumably would further decrease the concentration of DO. This possible effect of effluent nutrients was evaluated by laboratory .bioassays and by a comparison of mean annual biomasses in the estuary. A green algal population in vitro did increase in response to added effluent nutrients; however, the available field data suggest that a 46-percent increase in effluent discharge between 1965 and 1966 did not increase the estuary's phytoplankton biomass significantly.

Water Supply Paper↗
USGS1979

Histopathology of yearling sockeye salmon (Oncorhynchus nerka) infected with infectious hematopoietic necrosis (IHN)

Infectious hematopoietic necrosis (IHN) is generally believed to be a virus disease of very young salmonids. In recent years there have been increasing numbers of unpublished reports that this disease has been occurring uncharacteristically in fish as old as 7-14 months. Sockeye salmon (Oncorhynchus nerka) of this age the histological changes were not severe. Intestinal tract granular cells thought to be pathognomic in young fish were conspicuously absent. Kidney imprints showed necrobiotic bodies however, and subtle changes were observed in the spleen and kidney hematopoietic tissue.

Fish Pathology↗
USGS2019

Evaluating the potential for sea lice to evolve freshwater tolerance as a consequence of freshwater treatments in salmon aquaculture

Increasing usage of non-medicinal methods (NMMs) to control sea louse infestations on salmon farms has raised questions about whether sea lice may be able to evolve tolerance of NMMs. Of particular concern is the potential for sea lice to evolve freshwater tolerance as a result of freshwater treatments. Wild trout and some juvenile salmonids swim into freshwater to control infestations and regain ionic balance after disruption by sea lice; freshwater tolerance would compromise this potentially adaptive behavior. Here we evaluated the potential for freshwater tolerance to evolve in the sea louse Lepeophtheirus salmonis. When exposed to low-salinity water, parasitic stages of sea lice are able to osmoregulate through the host, while larval planktonic stages are not. Transcriptomic work suggests that sea lice mount a costly polygenic stress response when exposed to brackish water. The population structure of sea lice is panmictic in both the Pacific and Atlantic, making it conducive to rapid evolutionary responses. It is unknown how much heritable genetic variation these panmictic populations have for freshwater treatments. While usage of freshwater treatments on wellboats is increasing, it is unclear whether the freshwater itself is a strong selective force; during the freshwater exposure, sea lice can die from physical disruption during pumping and filtration on the wellboat. Future studies are advised to quantify the heritable variation in freshwater tolerance in sea louse populations, characterize mechanisms for freshwater tolerance in planktonic and attached sea lice, and assess the risk of freshwater tolerance evolution under different management strategies.

Aquaculture Environment Interactions↗