This dataset includes laboratory analyses of surface water samples and sediment trap material collected from (1) locations upstream, downstream, and within the Hells Canyon Complex (Idaho, Oregon) of the Snake River, (2) tributaries of the Snake River, and (3) two reservoirs near Boise, Idaho, from 2014 to 2022. The study area spans approximately 232 river miles of the Snake River and includes: two sites on the main stem of the Snake River upstream of the Hells Canyon Complex (Snake River mile 447.6, 399.0, and 345.6), six sites within Brownlee Reservoir (Snake River mile 318, 314, 310, 305, 300, and 286), one site within Oxbow Reservoir (Snake River mile 273), two sites within Hells Canyon Reservoir (Snake River mile 252 and 248.1), reservoir outflow locations (Snake River mile 283.9, 269.9, and 246.9), one location downstream of the Hells Canyon Complex (Snake River mile 215.4), and over 20 tributary sites of waterways discharging into the Snake River. In addition, the Lucky Peak and Anderson Ranch reservoirs along the Boise River were sampled in June and September 2018. At sites on the main stem of the Snake River, reservoir inflow and outflow locations of the Hells Canyon Complex, and tributaries of the Snake River, whole water and filtered surface water samples were collected by using either a depth-integrated sampler from bridges or submerging a polyethylene terephthalate (PETG) bottle (details for each site provided in the metadata file). Within reservoirs, whole water and filtered water samples were collected in profile from the surface (2 meters) to approximately 5 meters above the sediment-water interface using either a peristaltic pump or a Van Dorn sampler. Further, water up to 1 meter above the sediment-water interface was obtained by collecting water in vertical subsections above an undisturbed sediment core. Water samples were processed (details provided in the metadata file) and analyzed for total suspended solids (TSS), particulate total mercury (p.THg), particulate methylmercury (p.MeHg), particulate iron (p.Fe), particulate manganese (p.Mn), particulate organic carbon (POC) content and stable isotopic composition, particulate nitrogen (PN) content and stable isotopic composition, filter-passing total mercury (f.THg), filter-passing methylmercury (f.MeHg), dissolved organic carbon (DOC) concentration and stable isotopic composition, dissolved organic matter composition (UV-vis absorption and fluorescence spectroscopy; ultrahigh resolution mass spectrometry), inorganic anions (chloride, nitrate, sulfate, thiosulfate), acetate, major and trace elements, inorganic sulfide, and chlorophyll a. Dissolved organic matter UV-vis absorption measurements included the specific ultraviolet absorbance at 254 nanometers (SUVA254), spectral slopes (at 275 to 295 nm and 350 to 400 nm), and the spectral slope ratio. Dissolved organic matter fluorescence indices include the fluorescence index, humification index, and freshness index. Concentrations of particulate and filter-passing inorganic divalent mercury (p.Hg(II), f.Hg(II)) were calculated by subtracting p.MeHg and f.MeHg concentrations from p.THg and f.THg concentrations, respectively. Aqueous – particulate distribution coefficients (Kd values) for inorganic divalent mercury and methylmercury were determined. Suspended sediment was collected in settling traps deployed at up to three depths at 4 locations within the Hells Canyon Complex (Snake River mile 318, 300, 286, and 248; 16 deployments from September 2016 to September 2018); the depths targeted discrete epilimnetic, metalimnetic, and hypolimnetic regions of reservoirs. Settling trap material was sieved (less than and greater than 243 µm) and analyzed for total mercury, methylmercury, loss on ignition, organic carbon content and stable isotopic composition, nitrogen content and stable isotopic composition, trace and major element content, and mineralogical composition. In addition, measurements of water properties

This dataset includes laboratory analyses of surface water samples and sediment trap material collected from (1) locations upstream, downstream, and within the Hells Canyon Complex (Idaho, Oregon) of the Snake River, (2) tributaries of the Snake River, and (3) two reservoirs near Boise, Idaho, from 2014 to 2022. The study area spans approximately 232 river miles of the Snake River and includes: two sites on the main stem of the Snake River upstream of the Hells Canyon Complex (Snake River mile 447.6, 399.0, and 345.6), six sites within Brownlee Reservoir (Snake River mile 318, 314, 310, 305, 300, and 286), one site within Oxbow Reservoir (Snake River mile 273), two sites within Hells Canyon Reservoir (Snake River mile 252 and 248.1), reservoir outflow locations (Snake River mile 283.9, 269.9, and 246.9), one location downstream of the Hells Canyon Complex (Snake River mile 215.4), and over 20 tributary sites of waterways discharging into the Snake River. In addition, the Lucky Peak and Anderson Ranch reservoirs along the Boise River were sampled in June and September 2018. At sites on the main stem of the Snake River, reservoir inflow and outflow locations of the Hells Canyon Complex, and tributaries of the Snake River, whole water and filtered surface water samples were collected by using either a depth-integrated sampler from bridges or submerging a polyethylene terephthalate (PETG) bottle (details for each site provided in the metadata file). Within reservoirs, whole water and filtered water samples were collected in profile from the surface (2 meters) to approximately 5 meters above the sediment-water interface using either a peristaltic pump or a Van Dorn sampler. Further, water up to 1 meter above the sediment-water interface was obtained by collecting water in vertical subsections above an undisturbed sediment core. Water samples were processed (details provided in the metadata file) and analyzed for total suspended solids (TSS), particulate total mercury (p.THg), particulate methylmercury (p.MeHg), particulate iron (p.Fe), particulate manganese (p.Mn), particulate organic carbon (POC) content and stable isotopic composition, particulate nitrogen (PN) content and stable isotopic composition, filter-passing total mercury (f.THg), filter-passing methylmercury (f.MeHg), dissolved organic carbon (DOC) concentration and stable isotopic composition, dissolved organic matter composition (UV-vis absorption and fluorescence spectroscopy; ultrahigh resolution mass spectrometry), inorganic anions (chloride, nitrate, sulfate, thiosulfate), acetate, major and trace elements, inorganic sulfide, and chlorophyll a. Dissolved organic matter UV-vis absorption measurements included the specific ultraviolet absorbance at 254 nanometers (SUVA254), spectral slopes (at 275 to 295 nm and 350 to 400 nm), and the spectral slope ratio. Dissolved organic matter fluorescence indices include the fluorescence index, humification index, and freshness index. Concentrations of particulate and filter-passing inorganic divalent mercury (p.Hg(II), f.Hg(II)) were calculated by subtracting p.MeHg and f.MeHg concentrations from p.THg and f.THg concentrations, respectively. Aqueous – particulate distribution coefficients (Kd values) for inorganic divalent mercury and methylmercury were determined. Suspended sediment was collected in settling traps deployed at up to three depths at 4 locations within the Hells Canyon Complex (Snake River mile 318, 300, 286, and 248; 16 deployments from September 2016 to September 2018); the depths targeted discrete epilimnetic, metalimnetic, and hypolimnetic regions of reservoirs. Settling trap material was sieved (less than and greater than 243 µm) and analyzed for total mercury, methylmercury, loss on ignition, organic carbon content and stable isotopic composition, nitrogen content and stable isotopic composition, trace and major element content, and mineralogical composition. In addition, measurements of water properties

This dataset includes laboratory analyses of surface water samples and sediment trap material collected from (1) locations upstream, downstream, and within the Hells Canyon Complex (Idaho, Oregon) of the Snake River, (2) tributaries of the Snake River, and (3) two reservoirs near Boise, Idaho, from 2014 to 2019. The study area spans approximately 232 river miles of the Snake River and includes: sites on the main stem of the Snake River upstream of the Hells Canyon Complex (Snake River mile 447.6 and 345.6), four primary sites within Brownlee Reservoir (Snake River mile 318, 310, 300, and 286), one site within Oxbow Reservoir (Snake River mile 273), two sites within Hells Canyon Reservoir (Snake River mile 252 and 248.1), reservoir outflow locations (Snake River mile 283.9, 269.9, and 246.9), one location downstream of the Hells Canyon Complex (Snake River mile 215.4), and over 20 tributary sites of waterways discharging into the Snake River. In addition, the Lucky Peak and Anderson Ranch reservoirs along the Boise River were sampled in June and September 2018. At sites on the main stem of the Snake River, reservoir inflow and outflow locations of the Hells Canyon Complex, and tributaries of the Snake River, whole water and filtered surface water samples were collected by using either a depth-integrated sampler from bridges or submerging a polyethylene terephthalate (PETG) bottle (details for each site provided in the metadata file). Within reservoirs, whole water and filtered water samples were collected in profile from the surface (2 meters) to approximately 5 meters above the sediment-water interface using either a peristaltic pump or a Van Dorn sampler. Further, water up to 1 meter above the sediment-water interface was obtained by collecting water in vertical subsections above an undisturbed sediment core. Water samples were processed (details provided in the metadata file) and analyzed for total suspended solids (TSS), particulate total mercury (p.THg), particulate methylmercury (p.MeHg), particulate iron (p.Fe), particulate manganese (p.Mn), particulate organic carbon (POC) content and stable isotopic composition, particulate nitrogen (PN) content and stable isotopic composition, filter-passing total mercury (f.THg), filter-passing methylmercury (f.MeHg), dissolved organic carbon (DOC) concentration and stable isotopic composition, dissolved organic matter composition (UV-vis absorption and fluorescence spectroscopy; ultrahigh resolution mass spectrometry), inorganic anions (chloride, nitrate, sulfate, thiosulfate), acetate, major and trace elements, and inorganic sulfide. Dissolved organic matter UV-vis absorption measurements included the specific ultraviolet absorbance at 254 nanometers (SUVA254), spectral slopes (at 275 to 295 nm and 350 to 400 nm), and the spectral slope ratio. Dissolved organic matter fluorescence indices include the fluorescence index, humification index, and freshness index. Concentrations of particulate and filter-passing inorganic divalent mercury (p.Hg(II), f.Hg(II)) were calculated by subtracting p.MeHg and f.MeHg concentrations from p.THg and f.THg concentrations, respectively. Aqueous – particulate distribution coefficients (Kd values) for inorganic divalent mercury and methylmercury were determined. Suspended sediment was collected in settling traps deployed at up to three depths at 4 locations within the Hells Canyon Complex (Snake River mile 318, 300, 286, and 248; 16 deployments from September 2016 to September 2018); the depths targeted discrete epilimnetic, metalimnetic, and hypolimnetic regions of reservoirs. Settling trap material was sieved (less than and greater than 243 µm) and analyzed for total mercury, methylmercury, loss on ignition, organic carbon content and stable isotopic composition, nitrogen content and stable isotopic composition, trace and major element content, and mineralogical composition. There are 4 files (*.csv) provided in this product: 1) Table 1, site

This dataset includes laboratory analyses of surface water samples and sediment trap material collected from (1) locations upstream, downstream, and within the Hells Canyon Complex (Idaho, Oregon) of the Snake River, (2) tributaries of the Snake River, and (3) two reservoirs near Boise, Idaho, from 2014 to 2019. The study area spans approximately 232 river miles of the Snake River and includes: sites on the main stem of the Snake River upstream of the Hells Canyon Complex (Snake River mile 447.6 and 345.6), four primary sites within Brownlee Reservoir (Snake River mile 318, 310, 300, and 286), one site within Oxbow Reservoir (Snake River mile 273), two sites within Hells Canyon Reservoir (Snake River mile 252 and 248.1), reservoir outflow locations (Snake River mile 283.9, 269.9, and 246.9), one location downstream of the Hells Canyon Complex (Snake River mile 215.4), and over 20 tributary sites of waterways discharging into the Snake River. In addition, the Lucky Peak and Anderson Ranch reservoirs along the Boise River were sampled in June and September 2018. At sites on the main stem of the Snake River, reservoir inflow and outflow locations of the Hells Canyon Complex, and tributaries of the Snake River, whole water and filtered surface water samples were collected by using either a depth-integrated sampler from bridges or submerging a polyethylene terephthalate (PETG) bottle (details for each site provided in the metadata file). Within reservoirs, whole water and filtered water samples were collected in profile from the surface (2 meters) to approximately 5 meters above the sediment-water interface using either a peristaltic pump or a Van Dorn sampler. Further, water up to 1 meter above the sediment-water interface was obtained by collecting water in vertical subsections above an undisturbed sediment core. Water samples were processed (details provided in the metadata file) and analyzed for total suspended solids (TSS), particulate total mercury (p.THg), particulate methylmercury (p.MeHg), particulate iron (p.Fe), particulate manganese (p.Mn), particulate organic carbon (POC) content and stable isotopic composition, particulate nitrogen (PN) content and stable isotopic composition, filter-passing total mercury (f.THg), filter-passing methylmercury (f.MeHg), dissolved organic carbon (DOC) concentration and stable isotopic composition, dissolved organic matter composition (UV-vis absorption and fluorescence spectroscopy; ultrahigh resolution mass spectrometry), inorganic anions (chloride, nitrate, sulfate, thiosulfate), acetate, major and trace elements, and inorganic sulfide. Dissolved organic matter UV-vis absorption measurements included the specific ultraviolet absorbance at 254 nanometers (SUVA254), spectral slopes (at 275 to 295 nm and 350 to 400 nm), and the spectral slope ratio. Dissolved organic matter fluorescence indices include the fluorescence index, humification index, and freshness index. Concentrations of particulate and filter-passing inorganic divalent mercury (p.Hg(II), f.Hg(II)) were calculated by subtracting p.MeHg and f.MeHg concentrations from p.THg and f.THg concentrations, respectively. Aqueous – particulate distribution coefficients (Kd values) for inorganic divalent mercury and methylmercury were determined. Suspended sediment was collected in settling traps deployed at up to three depths at 4 locations within the Hells Canyon Complex (Snake River mile 318, 300, 286, and 248; 16 deployments from September 2016 to September 2018); the depths targeted discrete epilimnetic, metalimnetic, and hypolimnetic regions of reservoirs. Settling trap material was sieved (less than and greater than 243 µm) and analyzed for total mercury, methylmercury, loss on ignition, organic carbon content and stable isotopic composition, nitrogen content and stable isotopic composition, trace and major element content, and mineralogical composition. There are 4 files (*.csv) provided in this product: 1) Table 1, site

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).

Comma-separated values (.csv) file containing data related to mercury in biota collected from the Hells Canyon Reservoir Complex on the Snake River, Idaho and Oregon.

Comma-separated values (.csv) file containing data related to mercury in biota collected from the Hells Canyon Reservoir Complex on the Snake River, Idaho and Oregon.

This dataset includes field hydrologic measurements and laboratory analyses of surface and pore waters, sediments, benthic plants/biofilms, and biota along the Middle Snake River upgradient of the Hells Canyon Complex. The study region for this work focuses on a section of the Snake River heavily utilized for agriculture, with complex systems of irrigation diversion and return drainage, spanning 164 km above the Hells Canyon Complex (Idaho, Oregon). The goal of this study was to identify potential loading sources of methylmercury from the upgradient Snake River into the reservoir complex, with a focus on the tributaries, irrigation return drains, and riparian zones adjacent to agricultural lands along the river. To this end, 16 locations along the Snake River between River Miles 448 and 346 were sampled over a four-day period, July 11 – 14, 2022. At each sampling site, pore water and sediment cores were collected in the shallow riparian zones along the edge of the river, surface waters were collected from cross-sections of the river, river flow and velocity were measured, submerged macrophytes and associated biofilm was collected, and biota (snails, amphipods, clams, periphyton, dragonfly larvae) were sampled from shallow riparian margins using a boat-mounted benthic suction dredge. Concurrently, water samples were collected from the six major tributaries that enter the Snake River in the study reach (Succor Creek, Owyhee River, Boise River, Malheur River, Payette River, Weiser River) and from six irrigation return drains that were actively discharging to the Snake River. Data from additional irrigation return drains to the study reach, sampled in June 2021 and May 2022, are also included. All water samples (surface and pore water) were processed and analyzed for filter-passing total mercury and methylmercury, dissolved organic carbon (DOC), dissolved organic matter (DOM) composition (UV-vis absorption and fluorescence), inorganic anions (chloride, nitrate, sulfate), and filter acidified metals (iron, manganese). In addition, the surface waters were analyzed for total suspended solids (TSS), particulate total and methylmercury, particulate organic carbon (POC) and stable isotopic composition, particulate nitrogen (PN) content and stable isotopic composition, and particulate metals (iron, manganese); and the pore waters were analyzed for inorganic sulfide (S(-II)). Sediment, submerged macrophytes and biofilms, and biota samples were dried, ground, and analyzed for total and methylmercury. Loss on ignition was also measured on the sediment samples. This data release includes eight metadata and data tables in machine readable format (*.csv). All data columns in tables 3-8 are defined in Table 2. Reference Table 2 for associated units, abbreviation definitions, laboratory information, and method citations. Table_1_Site_Descriptions.csv - site descriptions Table_2_Analysis_Descriptions.csv - data dictionary defining column headings in Tables 3-8 Table_3_Water_SW.csv - surface water chemistry data Table_4_Water_PW.csv - pore water chemistry data Table_5_Sediment.csv - sediment chemistry data Table_6_Macrophytes_and_Biofilms.csv - submerged macrophyte and biofilm data Table_7_Hydrology.csv - hydrologic data Table_8_Biota.csv - biota data

This dataset describes biomass and methylmercury concentrations in zooplankton, other invertebrates, fish, and coarse and fine detritus samples collected at the outflow locations of Brownlee and Oxbow Reservoirs in the Snake River Hells Canyon Complex. Based on the sampling locations, the sampled materials were presumed to have flowed through the dam turbines or over the spillway, thereby representing biological export from the reservoirs. Samples were collected biweekly at each location over a sixteen-month period, June 2018 – September 2019. Sampling and analysis methods are described in the Processing Steps section of the metadata.

These data are comprised of measurements of elements (e.g., uranium, cobalt, nickel, copper, zinc, cadmium, lead, etc.), major anions (chloride, nitrite+nitrate as nitrogen, sulfate, etc.), organic carbon, and general water quality parameters measured in Pinyon Plain Mine containment pond water, sediment, vegetation, and aquatic invertebrate samples collected in calendar years 2023 and 2024.