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 descriptions 2) Table 2, data dictionary detailing terms used in Tables 3 and 4 3) Table 3, water chemistry data, and 4) Table 4, settling trap material data. A revision to this product at a later date will include additional measurements on sediment trap materials and water samples.