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 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

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 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

Data described herein was collected by USGS personnel and the project funded by USGS. Northern snakehead specimens were collected from the Potomac River and its tributaries by regional natural resource management agencies in the course of their field investigations working with this priority invasive aquatic species. Specimens were provided to USGS for the purpose of conducting health related assessments of northern snakehead in the region, with approximately 90 specimens evaluated grossly and histologically for the presence of lesions and abnormalities. Data presented here was collected seasonally (spring through fall) in 2006 and from 2015 to 2017. Data for each specimen includes date and location of collection, morphometrics, gender (if known), and gross abnormalities, and histological lesions observed. This body of data is stored in spreadsheet format.

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.

Environmental DNA detection results from samples collected using autonomous water sampling robots and manual approaches. Samples were collected in the Upper Yellowstone River (Montana) and Upper Snake River (Idaho/Wyoming) in 2018 and 2019. Samples were tested for the DNA of the following species: the waterborne protozoa Naegleria spp., the fish pathogen Tetracapsuloides bryosalmonae, Scomber japonicas (mackerel fish), kokanee salmon (Oncorhynchus nerka) and dreissenid mussel (Dreissena spp.).