This dataset includes the field measurements and laboratory analyses of surface water, seston, fish tissue, and sediment samples collected from Bighorn Lake, within Bighorn Canyon National Recreation area (BICA), during high flow (July 2015) and low flow (August 2016) conditions. The study area includes 7-9 sampling sites that follow a transect spanning the entire length of the reservoir from the Bighorn and Shoshone River inflows to the afterbay and tailwater below Yellowtail dam. Multiple samples were collected at each sampling site and usually included the top 2 cm of sediment at the sediment/water interface, 2 meters above the sediment/water interface, and 2 meters below the reservoir surface. Microbial samples were collected from the water column and sediment samples using sterile techniques and placed on dry ice for laboratory DNA analysis. The samples were analyzed with qPCR and high-throughput DNA sequencing analysis. The qPCR data are archived in the National Center for Biotechnology Information (NCBI) database at: https://www.ncbi.nlm.nih.gov/guide/all/. Water-quality sonde field measurements included specific conductivity, temperature, pH, dissolved oxygen, fluorescent dissolved organic matter, chlorophyll, and turbidity. These field measurements were collected at 16-18 sites at approximately 30 cm increments from the reservoir surface to the reservoir bottom. Discrete water-quality samples that were analyzed for various constituents including selenium and mercury by the U.S. Geological Survey are archived in the National Water Information System (NWIS) database at: https://maps.waterdata.usgs.gov/mapper/index.html. Fish samples were collected during May and June 2015 from throughout Bighorn Lake and in the tailwater below Yellowtail dam and assayed for total mercury, total selenium, and mercury/carbon/nitrogen isotopes.

These data were compiled to study mercury and selenium concentrations in fish species and assemblages in lotic waterbodies across the Upper Colorado River Basin. Data were compiled from State and Federal agencies. This data table contains raw concentration data, as well as standardized concentrations corrected for differences based on sample type (i.e., tissue type), species-specific bioaccumulation rates (Table S1), and fish size (Table S2). The data were used in linear mixed effects models to estimate average mercury and selenium concentration in fish species and in fish assemblages, including fish total length (cm), sampling location (Sub basin name and GPS coordinates), and sampling year (Figures 2,3, and 4 from manuscript).

These data were compiled to study mercury and selenium concentrations in fish species and assemblages in lotic waterbodies across the Upper Colorado River Basin. Data were compiled from State and Federal agencies. This data table contains raw concentration data, as well as standardized concentrations corrected for differences based on sample type (i.e., tissue type), species-specific bioaccumulation rates (Table S1), and fish size (Table S2). The data were used in linear mixed effects models to estimate average mercury and selenium concentration in fish species and in fish assemblages, including fish total length (cm), sampling location (Sub basin name and GPS coordinates), and sampling year (Figures 2,3, and 4 from manuscript).

This dataset includes the field measurements and laboratory analyses of surface water, seston, and sediment collected from Lake Powell, within Glen Canyon National Recreation area (GLCA), during high flow (May-June 2014) and low flow (August 2015) conditions. The study area includes 12-13 sampling sites that follow a transect spanning the entire length of the reservoir from the Colorado River inflow to the Glen Canyon dam, as well as the San Juan River arm, the Escalante River arm and West Canyon. Bed sediment samples were analyzed for mercury speciation, methylmercury production and degradation rates, total reduced sulfur, iron speciation, organic content, and 16S rRNA gene templates as a proxy for microbial abundances. Water samples were collected from 3-5 depths at each site and analyzed for: total mercury (filtered and particulate), methylmercury (filtered and particulate), dissolved organic and inorganic carbon with 13C isotopic ratios, nutrients, anions, cations, trace metals, particulate carbon (with 13C isotopic ratios) and particulate nitrogen (with 15N isotopic ratios). Water quality sonde (EXO) field measurements included specific conductivity, temperature, pH, dissolved oxygen, fluorescent dissolved organic matter, chlorophyll, and turbidity. Fish samples were also collected during November 2014 from Good Hope Bay (upper reservoir), Wahweap Bay (lower reservoir), and the San Juan arm and assayed for total mercury for comparison with previous striped bass samples collected by the state of Utah. There are nine files (*.csv) in this dataset: 1) data dictionary ; 2) sediment data; 3) water data; 4) seston data; 5) fish data; 6) EXO main channel profile data ; 7) EXO off channel profile data; 8) quality assurance data; and 9) molecular data.

This dataset includes the field measurements and laboratory analyses of surface water, seston, and sediment collected from Lake Powell, within Glen Canyon National Recreation area (GLCA), during high flow (May-June 2014) and low flow (August 2015) conditions. The study area includes 12-13 sampling sites that follow a transect spanning the entire length of the reservoir from the Colorado River inflow to the Glen Canyon dam, as well as the San Juan River arm, the Escalante River arm and West Canyon. Bed sediment samples were analyzed for mercury speciation, methylmercury production and degradation rates, total reduced sulfur, iron speciation, organic content, and 16S rRNA gene templates as a proxy for microbial abundances. Water samples were collected from 3-5 depths at each site and analyzed for: total mercury (filtered and particulate), methylmercury (filtered and particulate), dissolved organic and inorganic carbon with 13C isotopic ratios, nutrients, anions, cations, trace metals, particulate carbon (with 13C isotopic ratios) and particulate nitrogen (with 15N isotopic ratios). Water quality sonde (EXO) field measurements included specific conductivity, temperature, pH, dissolved oxygen, fluorescent dissolved organic matter, chlorophyll, and turbidity. Fish samples were also collected during November 2014 from Good Hope Bay (upper reservoir), Wahweap Bay (lower reservoir), and the San Juan arm and assayed for total mercury for comparison with previous striped bass samples collected by the state of Utah. There are nine files (*.csv) in this dataset: 1) data dictionary ; 2) sediment data; 3) water data; 4) seston data; 5) fish data; 6) EXO main channel profile data ; 7) EXO off channel profile data; 8) quality assurance data; and 9) molecular data.

The U.S. Geological Survey is studying Lake Koocanusa, a border reservoir between British Columbia in Canada and Montana, in collaboration with the Montana Department of Environmental Quality and the U.S. Environmental Protection Agency (Region 8). This work is part of a multi-agency project to apply an ecosystem-scale selenium modeling methodology (Presser and Luoma, 2010) to the lake to support development of a site-specific selenium guideline for the protection of aquatic life. This Data Release makes available measurements taken during the periods of May, 2015 to October, 2015 and April, 2016 to September, 2016. Spatially and temporally matched sets of dissolved and suspended particulate material selenium concentrations were collected mainly at two locations (forebay and international boundary) and at two depths (epilimnion, 3 meters below lake surface; hypolimnion, 3 meters above lake bottom). These data allow calculation of an environmental partitioning factor (i.e., Kd) between dissolved and suspended particulate material selenium concentrations as an initial modeling step. This Data Release contains 1) a location map; 2) a modeling schematic; 3) collection methods, analytical methods, and quality control information; 4) spreadsheets and graphical displays of selenium data; and 5) hydrological parameters related to sampling conditions at the lake. This Data Release will be updated and modified as additional sampling and analysis takes place.

The U.S. Geological Survey is studying Lake Koocanusa, a border reservoir between British Columbia in Canada and Montana, in collaboration with the Montana Department of Environmental Quality and the U.S. Environmental Protection Agency (Region 8). This work is part of a multi-agency project to apply an ecosystem-scale selenium modeling methodology (Presser and Luoma, 2010) to the lake to support development of a site-specific selenium guideline for the protection of aquatic life. This Data Release makes available measurements taken during the periods of May, 2015 to October, 2015 and April, 2016 to September, 2016. Spatially and temporally matched sets of dissolved and suspended particulate material selenium concentrations were collected mainly at two locations (forebay and international boundary) and at two depths (epilimnion, 3 meters below lake surface; hypolimnion, 3 meters above lake bottom). These data allow calculation of an environmental partitioning factor (i.e., Kd) between dissolved and suspended particulate material selenium concentrations as an initial modeling step. This Data Release contains 1) a location map; 2) a modeling schematic; 3) collection methods, analytical methods, and quality control information; 4) spreadsheets and graphical displays of selenium data; and 5) hydrological parameters related to sampling conditions at the lake. This Data Release will be updated and modified as additional sampling and analysis takes place.

Working in cooperation with EPA, the USGS coordinated the collection of fish tissue for processing and analyses by the EPA Region 10 Manchester Environmental Laboratory located in Port Orchard, WA. This effort was being tied to existing operations work performed by state wildlife agencies in Idaho and Montana (Ross et al. 2018). Annually, in late August and September, the Idaho Department of Fish and Game (IDFG), the Montana Department of Fish, Wildlife and Parks (MTFWP), and the Kootenai Tribe of Idaho conduct population surveys on the Kootenai River. During the 2018 electrofishing population surveys, state wildlife agency personnel also retained collected fish for this effort. The following were key design components of fish collection in the Kootenai River: (1) Fish were caught and analyzed for selenium and mercury in multiple tissues (filet, whole body, and/or egg/ovaries) as available to assess baseline contamination/bioaccumulation in fish species between Libby Dam and downstream of Bonners Ferry, ID. (2) Fish were caught from the mainstem Kootenai River in early September 2018 and analyzed for selenium and mercury from immediately downstream of Libby Dam (tailwater), downstream of Troy, MT, downstream of the ID/MT border, and in the proximity of Shorty’s Island downstream of Bonner’s Ferry. (3) The EPA Region 10 laboratory provided in-kind support for selenium and mercury analyses for the 142 fish samples collected. EPA Region 10 also provided data and sample management support via the Scribe Project Manager (RSCC). More details of the study design are given by USEPA and USGS (2018). Results: A total of 142 fish representing 13 species were retained for tissue analysis. Eggs were obtained from two species, kokanee salmon and mountain whitefish. In kokanee salmon, eggs were found in two fish from only site KR13 (Kootenai River below Libby Dam) and ranged from 4.17 to 5.01 mg/kg selenium as dry weight (dw). Eggs were found in mountain whitefish from all sites except the most downstream site sampled, KR4 (Kootenai River near Shorty’s Island). Selenium concentrations in mountain whitefish eggs ranged from 11.6 to 24.8 mg/kg (dw). An objective of the study was to compare selenium concentrations in fish and water to USEPA nationally recommended water quality criteria for selenium. The national criteria recommend that concentrations in fish eggs not exceed 15.1 mg/kg (dw), concentrations in whole-body of fish not exceed 8.5 mg/kg dry weight, or (b) concentrations in muscle tissue not exceed 11.3 mg/kg dry weight (USEPA 2016). For eggs, 6 of the 8 mountain whitefish egg samples exceeded EPA’s recommended value. No samples exceeded the whole-body criterion component of 8.5 mg/kg dry weight and no samples exceeded the muscle criterion component of 11.3 mg/kg dry weight. References: Ross, T.J., K. McDonnell, R. Hardy, and S. Stephenson. 2018. Kootenai River resident fish mitigation: white sturgeon, burbot, native salmonid monitoring and evaluation (Annual Progress Report May 1, 2016 — April 31, 2017). BPA Project # 1988-065-00, Idaho Department of Fish and Game. Report to the Bonneville Power Administration, Environment, Fish and Wildlife, Portland, OR. 118 pp. https://www.cbfish.org. USEPA. 2016. Aquatic Life Ambient Water Quality Criterion for Selenium – Freshwater 2016. 822-R-16-006, U.S. Environmental Protection Agency. 807 pp. https://www.epa.gov/wqc/aquatic-life-criterion-selenium [Accessed February 21, 2018]. USEPA and USGS. 2018. Kootenai River Fish Tissue Study Quality Assurance Project Plan. Prepared by U.S. Environmental Protection Agency, Regions 8 and 10, and U.S. Geological Survey, Idaho Water Science Center. 28 August 2018 (Revised 01 October 2018). 41 pp.

Working in cooperation with EPA, the USGS coordinated the collection of fish tissue for processing and analyses by the EPA Region 10 Manchester Environmental Laboratory located in Port Orchard, WA. This effort was being tied to existing operations work performed by state wildlife agencies in Idaho and Montana (Ross et al. 2018). Annually, in late August and September, the Idaho Department of Fish and Game (IDFG), the Montana Department of Fish, Wildlife and Parks (MTFWP), and the Kootenai Tribe of Idaho conduct population surveys on the Kootenai River. During the 2018 electrofishing population surveys, state wildlife agency personnel also retained collected fish for this effort. The following were key design components of fish collection in the Kootenai River: (1) Fish were caught and analyzed for selenium and mercury in multiple tissues (filet, whole body, and/or egg/ovaries) as available to assess baseline contamination/bioaccumulation in fish species between Libby Dam and downstream of Bonners Ferry, ID. (2) Fish were caught from the mainstem Kootenai River in early September 2018 and analyzed for selenium and mercury from immediately downstream of Libby Dam (tailwater), downstream of Troy, MT, downstream of the ID/MT border, and in the proximity of Shorty’s Island downstream of Bonner’s Ferry. (3) The EPA Region 10 laboratory provided in-kind support for selenium and mercury analyses for the 142 fish samples collected. EPA Region 10 also provided data and sample management support via the Scribe Project Manager (RSCC). More details of the study design are given by USEPA and USGS (2018). Results: A total of 142 fish representing 13 species were retained for tissue analysis. Eggs were obtained from two species, kokanee salmon and mountain whitefish. In kokanee salmon, eggs were found in two fish from only site KR13 (Kootenai River below Libby Dam) and ranged from 4.17 to 5.01 mg/kg selenium as dry weight (dw). Eggs were found in mountain whitefish from all sites except the most downstream site sampled, KR4 (Kootenai River near Shorty’s Island). Selenium concentrations in mountain whitefish eggs ranged from 11.6 to 24.8 mg/kg (dw). An objective of the study was to compare selenium concentrations in fish and water to USEPA nationally recommended water quality criteria for selenium. The national criteria recommend that concentrations in fish eggs not exceed 15.1 mg/kg (dw), concentrations in whole-body of fish not exceed 8.5 mg/kg dry weight, or (b) concentrations in muscle tissue not exceed 11.3 mg/kg dry weight (USEPA 2016). For eggs, 6 of the 8 mountain whitefish egg samples exceeded EPA’s recommended value. No samples exceeded the whole-body criterion component of 8.5 mg/kg dry weight and no samples exceeded the muscle criterion component of 11.3 mg/kg dry weight. References: Ross, T.J., K. McDonnell, R. Hardy, and S. Stephenson. 2018. Kootenai River resident fish mitigation: white sturgeon, burbot, native salmonid monitoring and evaluation (Annual Progress Report May 1, 2016 — April 31, 2017). BPA Project # 1988-065-00, Idaho Department of Fish and Game. Report to the Bonneville Power Administration, Environment, Fish and Wildlife, Portland, OR. 118 pp. https://www.cbfish.org. USEPA. 2016. Aquatic Life Ambient Water Quality Criterion for Selenium – Freshwater 2016. 822-R-16-006, U.S. Environmental Protection Agency. 807 pp. https://www.epa.gov/wqc/aquatic-life-criterion-selenium [Accessed February 21, 2018]. USEPA and USGS. 2018. Kootenai River Fish Tissue Study Quality Assurance Project Plan. Prepared by U.S. Environmental Protection Agency, Regions 8 and 10, and U.S. Geological Survey, Idaho Water Science Center. 28 August 2018 (Revised 01 October 2018). 41 pp.

The Hells Canyon Complex (HCC) is comprised of a series of three consecutive reservoirs (Brownlee, Oxbow, and Hells Canyon) along a 145 km reach of the Snake River bordered by Idaho to the east and Oregon to the west. Due to concerns regarding mercury (Hg) contamination within the HCC, in cooperation with Idaho Power Company, the U.S. Geological Survey has been leading an investigation into the sources, transport, microbial transformations, chemical speciation and bioaccumulation of Hg in this complex river-reservoir environment. This data release is focused on the sediment component of this larger effort and includes data collected between 2014 and 2018 from shallow surface sediment (≤ top 5 cm) and from sectioned deep cores ranging from 34 cm to 112 cm in length. While the majority of the data was collected from within the HCC, some limited additional data is included from a number of riverine bed sediment sites located in the watershed upstream of the HCC and from two additional reservoirs on the Boise River sampled as control sites (Anderson Ranch and Lucky Peak reservoirs). For shallow surface sediment, the list of mercury associated analytes reported in this dataset includes total mercury, methylmercury, and inorganic reactive mercury concentrations; as well as rate constants and calculated potential rates associated with microbial methylmercury production and degradation, derived from stable isotope amendment bottle incubations. The list of non-mercury analytes includes field measurements of temperature, oxidation-reduction potential and pH; percent dry weight; percent loss on ignition; wet bulk density; porosity; total reduced sulfur; and iron speciation. For a sub-set of the shallow sediment sampled there is additional data for: percent organic carbon (with isotopic 13C values), percent nitrogen (with isotopic 15N values), and grain size (percent < 64 µm). Of the eight sampling events conducted within the HCC, sediment porewater samples were collected from sediment-water interface cores on three occasions to estimate benthic-pelagic diffusive fluxes of a number of mercury and non-mercury constituents. The list of porewater analytes determined and reported herein include: total mercury, methylmercury, ortho-phosphate, ammonium, sulfide, dissolved organic carbon, dissolved organic matter specific ultra-violet absorption at 254 nm (SUVA254), acetate, sulfate, thiosulfate, nitrate, and elemental analysis of Al, As, B, Br, Ca, Cd, Cl, Cu, F, Fe, K, Mg, Mn, Mo, Na, Ni, P, Pb, Se, Si (as SiO2), U, and Zn. Of the eleven deep cores collected and sub-sectioned, all sediment samples were assayed for total mercury and percent loss on ignition, nine were assayed for methylmercury, and two were assayed for dry particle density and environmental radionuclides (137Cs, 210Pb and 226Ra) to assess sedimentation rates. This data release includes five data tables given both as Excel (*.xlsx) and machine readable 'comma-separated values' format (*.csv): 1) ‘T1_Data.Dictionary_HCC.2014-18’, the Data Dictionary, which provides definitions and details related to the other four data tables and includes analytical methods citations; 2) ‘T2_Shallow sed bulk_HCC.2014-18’, the shallow (bulk) sediment dataset; 3) ‘T3_Shallow sed porewater_HCC.2014-18’, the shallow sediment porewater dataset; 4) ‘T4_Deep cores_HCC.2014-18’, the deep core profile dataset; and 5) ‘T5_QA_HCC.2014-18’, quality assurance data summary for all major analyses. In addition, file ‘HCC 2014-18.kmz’ provides the sampling locations in a machine-readable geospatial file format (*.kmz).