Clear Lake is a 180 km2 freshwater lake located approximately 120 km northwest of Sacramento in the California Coast Range. The lake is a popular sport-fishing destination, however, there are fish consumption advisories associated with mercury (Hg) contamination for several species. The lake has three arms: a large open-water region to the northwest (Upper Arm), a smaller and narrower region to the southeast (Lower Arm), and the smallest and narrowest region to the east (Oaks Arm). The Sulfur Bank Mercury Mine (SBMM), located on the eastern shore of the Oaks Arm, was mined by underground methods starting in the 1870s and then open-pit methods during the 1920s to 1950s. Since 1992, the SBMM has been a Superfund site managed by the U.S. Environmental Protection Agency. This former Hg mining area is thought to be the dominant contributor of Hg to Clear Lake and is the focus of continued remediation to minimize Hg impacts to Clear Lake. The SBMM area is an active geothermal area with springs and gas fumaroles. Clear Lake is eutrophic to hypereutrophic, based on elevated concentrations of nutrients (various forms of nitrogen, N, and phosphorus, P) that cause excessive algal blooms and periodic fish kills. There are current studies underway (by the University of California, Davis, UCD) to improve the understanding of nutrient cycling within the lake. The UCD group is developing a three-dimensional hydrodynamic computer model (https://resources.ca.gov/-/media/CNRA-Website/Files/Initiatives/Blue-Ribbon-Committee-for-the-Rehabilitation-of-Clear-Lake/2022-BRC-Annual-Report-_20230110_DraftFinal.pdf ) of the lake that simulates periodic stratification of temperature and dissolved oxygen as well as nutrient dynamics. An effort is planned during 2023-2025 to add mercury cycling to the 3-D model. Monitoring and modeling efforts are being implemented to improve understanding of the ways that nutrient dynamics affect the cycling, transport and bioaccumulation of Hg, which remains poorly understood. This data release documents the results of water-quality sampling during June 2020 through June 2022. It includes three data tables given as machine readable 'comma-separated values' format (*.csv): 1) ‘T1_CL_DataDictionary’, the Data Dictionary, which provides definitions and details related to the other two data tables and includes citations of analytical methods; 2) ‘T2_CL_Discrete_SW’, the discrete-sample surface-water dataset including concentration data for Hg species (including total mercury and methylmercury in dissolved and particulate forms) and nutrients (including several forms of N and P); and 3) ‘T3_CL_QA_SW’, a quality assurance data summary for the discrete water samples. In addition, file ‘Clear Lake Coordinates_SW 2020-22_052324’ provides the sampling locations in a machine-readable geospatial file format (*.kmz).

Clear Lake is a 180 km2 freshwater lake located in the California Coast Range, approximately 120 km northwest of Sacramento. The lake supports a wide variety of fish and bird species and is a very popular sport-fishing destination. However, fish consumption advisories associated with mercury (Hg) contamination exist for several popular recreational species. The lake is comprised of three main regions including a large open-water region to the northwest (North Arm), a smaller and narrower region to the southeast (South Arm), and the smallest and narrowest region to the east (Oaks Arm). The Sulfur Bank Mercury Mine (SBMM), located on the south shore of the Oaks Arm, was mined by both open-pit and underground methods (intermittently active from the 1870s until 1957), and is now a U.S. Environmental Protection Agency (USEPA) Superfund site. This former Hg mining area represents a dominant contributor of Hg to the adjacent lake and is the focus of continued clean-up efforts to minimize Hg impacts to Clear Lake. The SBMM area is also host to active hot springs and gas fumaroles. Clear Lake is classified as eutrophic to hypereutrophic, based on high levels of nutrients (various forms of nitrogen, N, and phosphorus, P) that cause excessive algal blooms and periodic fish kills. There are current studies underway (by the Univ. of California, Davis, UCD) to improve the understanding of nutrient cycling within the lake. The way in which nutrient dynamics affect the cycling, transport and bioaccumulation of Hg remains poorly understood. Because of the expense and human resources required to conduct traditional water-quality studies, and the knowledge that water quality may vary significantly on an hourly or daily time scale in some locations, there is a need to develop more spatially and temporally robust monitoring programs to study both mercury and nutrients within Clear Lake and elsewhere. Recent advances in deployable in-situ electrochemical and optical sensors, as well as remote-sensing approaches, offer an opportunity to collect critical water-quality data at high temporal and spatial resolution to a degree previously unobtainable. However, these approaches require a detailed examination of the relationships between the constituent of concern (for example, the concentration of suspended sediment or various Hg species) and the electrochemical or optical properties of water for which the current class of sensors are best suited (for example, turbidity, dissolved organic carbon, or algal concentration). This preliminary study of particulate and filtered Hg species (including total mercury and methylmercury) and non-Hg water-column constituents was designed to lay the groundwork for developing a more robust Hg monitoring program for Clear Lake. This data release documents the results from a single (2-day) sampling event during July 2019 that focused on the collection of two types of surface-water data: a) discrete samples collected with a Van Dorn style sampler for a suite of Hg and non-Hg water constituents collected near the surface (1 m depth) and near bottom (approximately 1 m off of the bottom); and b) continuous vertical profiles collected in-situ with a water-quality sonde (electrochemical / optical probe data). Five of the nine discrete sample locations were co-located with fixed monitoring stations (moorings) being used by UCD for the study of nutrients within Clear Lake. Sampling included all 3 lake regions, including the Upper Arm (3 discrete-sample sites and 9 vertical-profile sites), the Lower Arm (3 discrete-sample sites and 9 vertical-profile sites), and the Oaks Arm (3 discrete-sample sites and 3 vertical-profile sites). This data release includes four data tables given both as Excel (*.xlsx) and machine readable 'comma-separated values' format (*.csv): 1) ‘T1_Data.Dictionary_CL_07.2019’, the Data Dictionary, which provides definitions and details related to the other three data tables and includes citations of analytical

Clear Lake is a 180 km2 freshwater lake located in the California Coast Range, approximately 120 km northwest of Sacramento. The lake supports a wide variety of fish and bird species and is a very popular sport-fishing destination. However, fish consumption advisories associated with mercury (Hg) contamination exist for several popular recreational species. The lake is comprised of three main regions including a large open-water region to the northwest (North Arm), a smaller and narrower region to the southeast (South Arm), and the smallest and narrowest region to the east (Oaks Arm). The Sulfur Bank Mercury Mine (SBMM), located on the south shore of the Oaks Arm, was mined by both open-pit and underground methods (intermittently active from the 1870s until 1957), and is now a U.S. Environmental Protection Agency (USEPA) Superfund site. This former Hg mining area represents a dominant contributor of Hg to the adjacent lake and is the focus of continued clean-up efforts to minimize Hg impacts to Clear Lake. The SBMM area is also host to active hot springs and gas fumaroles. Clear Lake is classified as eutrophic to hypereutrophic, based on high levels of nutrients (various forms of nitrogen, N, and phosphorus, P) that cause excessive algal blooms and periodic fish kills. There are current studies underway (by the Univ. of California, Davis, UCD) to improve the understanding of nutrient cycling within the lake. The way in which nutrient dynamics affect the cycling, transport and bioaccumulation of Hg remains poorly understood. Because of the expense and human resources required to conduct traditional water-quality studies, and the knowledge that water quality may vary significantly on an hourly or daily time scale in some locations, there is a need to develop more spatially and temporally robust monitoring programs to study both mercury and nutrients within Clear Lake and elsewhere. Recent advances in deployable in-situ electrochemical and optical sensors, as well as remote-sensing approaches, offer an opportunity to collect critical water-quality data at high temporal and spatial resolution to a degree previously unobtainable. However, these approaches require a detailed examination of the relationships between the constituent of concern (for example, the concentration of suspended sediment or various Hg species) and the electrochemical or optical properties of water for which the current class of sensors are best suited (for example, turbidity, dissolved organic carbon, or algal concentration). This preliminary study of particulate and filtered Hg species (including total mercury and methylmercury) and non-Hg water-column constituents was designed to lay the groundwork for developing a more robust Hg monitoring program for Clear Lake. This data release documents the results from a single (2-day) sampling event during July 2019 that focused on the collection of two types of surface-water data: a) discrete samples collected with a Van Dorn style sampler for a suite of Hg and non-Hg water constituents collected near the surface (1 m depth) and near bottom (approximately 1 m off of the bottom); and b) continuous vertical profiles collected in-situ with a water-quality sonde (electrochemical / optical probe data). Five of the nine discrete sample locations were co-located with fixed monitoring stations (moorings) being used by UCD for the study of nutrients within Clear Lake. Sampling included all 3 lake regions, including the Upper Arm (3 discrete-sample sites and 9 vertical-profile sites), the Lower Arm (3 discrete-sample sites and 9 vertical-profile sites), and the Oaks Arm (3 discrete-sample sites and 3 vertical-profile sites). This data release includes four data tables given both as Excel (*.xlsx) and machine readable 'comma-separated values' format (*.csv): 1) ‘T1_Data.Dictionary_CL_07.2019’, the Data Dictionary, which provides definitions and details related to the other three data tables and includes citations of analytical

Samples were collected from Clear Lake, California from 2019-2022 by the U.S. Geological Survey (USGS) California Water Science Center, the USGS Forest and Rangeland Ecosystem Science Center (FRESC), the US Environmental Protection Agency, and EA Engineering Science and Technology Inc. to assess the extent and cycling of legacy mercury (Hg) contamination from Sulphur Bank Mine. Samples of waste rock, sediments, groundwater, and biological tissue (zooplankton, bluegill, smallmouth bass, Mississippi silversides, and largemouth bass) were analyzed for Hg stable isotopes by the U.S. Geological Survey Mercury Research Laboratory. Mercury concentrations for sediments, waste rocks, and groundwaters are included within this data release and information for biological Hg concentrations can be found in the companion data release (https://doi.org/10.5066/P96912PN).

Samples were collected from Clear Lake, California from 2019-2022 by the U.S. Geological Survey (USGS) California Water Science Center, the USGS Forest and Rangeland Ecosystem Science Center (FRESC), the US Environmental Protection Agency, and EA Engineering Science and Technology Inc. to assess the extent and cycling of legacy mercury (Hg) contamination from Sulphur Bank Mine. Samples of waste rock, sediments, groundwater, and biological tissue (zooplankton, bluegill, smallmouth bass, Mississippi silversides, and largemouth bass) were analyzed for Hg stable isotopes by the U.S. Geological Survey Mercury Research Laboratory. Mercury concentrations for sediments, waste rocks, and groundwaters are included within this data release and information for biological Hg concentrations can be found in the companion data release (https://doi.org/10.5066/P96912PN).

Clear Lake, located within the Coast Range west of California’s Central Valley, is the largest natural freshwater lake contained fully within the state and geologically is considered to be the oldest lake in North America. Clear Lake is popular for recreation and provides critical habitat to a wide variety of fish and bird species. Water quality in Clear Lake is degraded by both by mercury contamination and harmful algal blooms (HABs). The mercury contamination is largely associated with the Sulfur Bank Mercury Mine (SBMM), located on the eastern shore of the Oaks Arm in the northeastern portion of the Lake. The mine was operated intermittently from the 1870s until 1957 and is now a U.S. Environmental Protection Agency (USEPA) Superfund site. Mercury contamination from SBMM and its biogeochemical mercury cycling within the lake are the focus of research being conducted by the U.S. Geological Survey (USGS) in cooperation with USEPA. The HABs are associate with excessive nutrient eutrophication within the lake; nutrient cycling and the distribution of oxic and anoxic conditions within the water column are active areas of investigation by researchers at the University of California at Davis (UCD). This product represents the results of a collaboration between USGS and UCD scientists which focuses on analyses of mercury speciation in shallow sediment cores from Clear Lake that were experimentally manipulated with respect to overlying water redox conditions. Twenty-four shallow sediment cores (up to 25 cm deep) were initially collected by the UCD research team as part of their research efforts that focused on measuring nitrogen and phosphorus flux from the sediment to the overlying water under experimentally controlled oxic and anoxic conditions. The cores were collected in sets of four per site and were sampled from six unique sites around the lake, including: three from the northwestern area (Upper Arm,UA), one from the southeastern area (Lower Arm, LA), one from the northeastern area (Oaks Arm, OA), and one from the ‘narrows’ (NR) that hydrologically connects the UA and the OA. The cores were incubated for 30 days under laboratory controlled oxic or anoxic overlying water conditions (two cores per site per treatment) for the purposes of the UCD nutrient flux experiments. Upon completion of these experiments, each core was vertically sectioned into 2-cm or 5-cm intervals and preserved for additional analyses. A sample split for each sediment interval was collected, preserved frozen, and shipped to the USGS research group for the analyses presented in this data release product. The results of the UCD nutrient flux experiments are not presented as part of this product and will be published elsewhere by the UCD team. The USGS researchers subsequently sub-sampled and analyzed the uppermost sediment layer (top 0-2 cm interval) from all 24 previously incubated cores for the following constituents: total mercury, methylmercury, reactive divalent inorganic mercury, acid-extractable ferrous iron, poorly crystalline (amorphous) ferric iron, crystalline ferric iron, total reduced sulfur, organic content (as determined by loss on ignition), and percent dry weight. In addition, four cores (one each from the UA, LA, OA, and NR areas) were selected for analysis of total mercury, organic content, and percent dry weight at all depth intervals sampled. Further details regarding initial core collection, incubation conditions and analyses conducted by the USGS are provided in the metadata section of this product. This product includes three data tables given as machine readable 'comma-separated values' format (*.csv): 1) ‘T1_Data_Dictionary_CL_SED_2019’, the Data Dictionary, which provides definitions and details related to the other two data tables and includes citations of analytical methods; 2) ‘T2_Data_CL_SED_2019’, the primary sediment results dataset for the constituents described above; and 3) ‘T3_QA_CL_SED_2019’, a summary of quality

Clear Lake, located within the Coast Range west of California’s Central Valley, is the largest natural freshwater lake contained fully within the state and geologically is considered to be the oldest lake in North America. Clear Lake is popular for recreation and provides critical habitat to a wide variety of fish and bird species. Water quality in Clear Lake is degraded by both by mercury contamination and harmful algal blooms (HABs). The mercury contamination is largely associated with the Sulfur Bank Mercury Mine (SBMM), located on the eastern shore of the Oaks Arm in the northeastern portion of the Lake. The mine was operated intermittently from the 1870s until 1957 and is now a U.S. Environmental Protection Agency (USEPA) Superfund site. Mercury contamination from SBMM and its biogeochemical mercury cycling within the lake are the focus of research being conducted by the U.S. Geological Survey (USGS) in cooperation with USEPA. The HABs are associate with excessive nutrient eutrophication within the lake; nutrient cycling and the distribution of oxic and anoxic conditions within the water column are active areas of investigation by researchers at the University of California at Davis (UCD). This product represents the results of a collaboration between USGS and UCD scientists which focuses on analyses of mercury speciation in shallow sediment cores from Clear Lake that were experimentally manipulated with respect to overlying water redox conditions. Twenty-four shallow sediment cores (up to 25 cm deep) were initially collected by the UCD research team as part of their research efforts that focused on measuring nitrogen and phosphorus flux from the sediment to the overlying water under experimentally controlled oxic and anoxic conditions. The cores were collected in sets of four per site and were sampled from six unique sites around the lake, including: three from the northwestern area (Upper Arm,UA), one from the southeastern area (Lower Arm, LA), one from the northeastern area (Oaks Arm, OA), and one from the ‘narrows’ (NR) that hydrologically connects the UA and the OA. The cores were incubated for 30 days under laboratory controlled oxic or anoxic overlying water conditions (two cores per site per treatment) for the purposes of the UCD nutrient flux experiments. Upon completion of these experiments, each core was vertically sectioned into 2-cm or 5-cm intervals and preserved for additional analyses. A sample split for each sediment interval was collected, preserved frozen, and shipped to the USGS research group for the analyses presented in this data release product. The results of the UCD nutrient flux experiments are not presented as part of this product and will be published elsewhere by the UCD team. The USGS researchers subsequently sub-sampled and analyzed the uppermost sediment layer (top 0-2 cm interval) from all 24 previously incubated cores for the following constituents: total mercury, methylmercury, reactive divalent inorganic mercury, acid-extractable ferrous iron, poorly crystalline (amorphous) ferric iron, crystalline ferric iron, total reduced sulfur, organic content (as determined by loss on ignition), and percent dry weight. In addition, four cores (one each from the UA, LA, OA, and NR areas) were selected for analysis of total mercury, organic content, and percent dry weight at all depth intervals sampled. Further details regarding initial core collection, incubation conditions and analyses conducted by the USGS are provided in the metadata section of this product. This product includes three data tables given as machine readable 'comma-separated values' format (*.csv): 1) ‘T1_Data_Dictionary_CL_SED_2019’, the Data Dictionary, which provides definitions and details related to the other two data tables and includes citations of analytical methods; 2) ‘T2_Data_CL_SED_2019’, the primary sediment results dataset for the constituents described above; and 3) ‘T3_QA_CL_SED_2019’, a summary of quality

This dataset includes water-quality data for samples collected at sixteen sites in the Clear Lake Drainage Basin, Lake County, California, between November 2018 and March 2024. Sampling in the reach of the Scotts Creek drainage below the confluence with South Fork Scotts Creek (USGS stations 11448800 and 390236122575901) was done during November 2018 to May 2019 (water year 2019; water years (WYs) begin Oct. 1 and end Sept. 30, for example water year 2024 began on Oct. 1, 2023), and also during WYs 2021-24. Sampling at South Fork Scotts Creek near Lakeport (11448750) and Scotts Creek at Eickhoff Road Bridge near Lakeport (390544122574201) was done during WYs 2021-24. Sites on several creeks in the basin were sampled during WYs 2022-24: Clover Creek Bypass at Elk Mountain Road (11449235), Cole Creek at Kelseyville (11449820), Kelsey Creek near Kelseyville (11449500), Kelsey Creek above Soda Bay Road near Kelseyville (390030122502101), and Middle Creek at Rancheria Road (391057122544301). Two sites on Middle Creek were sampled only during WYs 2022-23: Middle Creek Near Vann (391448122565601) and Middle Creek below Elk Mountain Road near Upper Lake (391227122553101). Two sites on Adobe Creek (390054122521501 and 390054122532801) were sampled only during WY 2023. Two sites on Scotts Creek below Tule Lake (11390936122551901 and 11449255) were sampled during WY2021 and WYs 2023-24, respectively, and a site on Molesworth Creek (11449370) was sampled during WYs 2023-24. Sampling events targeted high flows after rain events as well as some lower flow baseline conditions during the wet season (typically December through April) during WYs 2022, 2023, and 2024. Two different sets of analyses (schedules A and B) were assigned to selected sampling sites. Schedule A (116 samples at 6 sites samples during WYs 2022-24), the most complete, included mercury (Hg) species (total Hg (THg) and methylmercury (MeHg), both filtered and particulate), dissolved organic carbon (DOC) and optical properties, filtered and unfiltered nutrients (various forms of nitrogen (N) and phosphorus (P)), and total suspended sediment (TSS). Schedule B (148 samples at 10 sites) consisted of similar analyses as Schedule A but without mercury species, DOC, or optical properties. Stable isotopes of nitrogen and oxygen in dissolved nitrate were analyzed in selected samples from WYs 2022-23. The median and mean grain-size of suspended sediment in selected samples are also reported.

This dataset includes field measurements and laboratory analyses of surface water, bottom water (sediment-water interface), surficial (0-2 cm) sediment, pore water (0-2 cm), and biota collected in Lake Combie, California, from September 2017 through August 2021. The study area includes six sites within the reservoir where discrete samples of surface water, bottom water, sediment, and pore water were taken along the length of the reservoir at the following distances from the spillway: 0.07 miles, 0.5 miles, 0.9 miles, 1.2 miles, 1.3 miles, and 1.4 miles. The within-reservoir sites were sampled during September 2017, February 2018, and May 2018, prior to a large sediment removal operation, and again during September 2019, February 2020, and June 2020 following the removal operation. Zooplankton samples were collected at four of the six sites during the sampling period. Fish were collected from within two regions of the lake: in the Wooley Creek arm of the lower reservoir, and in the upper reservoir near the targeted area for sediment removal operations. Vertical profiles of water quality were measured with a multi-parameter sonde during water collection events and during one zooplankton event. Thirty-six surface water and thirty-six bottom water samples were collected at each site and analyzed for total mercury (filtered and particulate), methylmercury (filtered and particulate), total suspended solids, sulfate, chloride, selected dissolved nutrients, particulate 13-C/12-C and 15-N/14-N isotopic ratios, total particulate carbon and nitrogen, particulate carbon to nitrogen molar ratio, dissolved organic carbon, and dissolved organic-matter properties (absorption and fluorescence). Thirty-six bed-sediment samples were analyzed for total mercury, methylmercury, total reduced sulfur, and organic content. Pore water extracted from bed sediment was analyzed for filtered total mercury, filtered methylmercury, sulfate, chloride, selected dissolved nutrients, and dissolved organic carbon. Surface water, bottom water, and sediment collections included an additional four field replicates each for analysis - pore water had six replicates. One hundred six zooplankton samples and twenty-three replicates were analyzed for total mercury, methylmercury, 13-C/12-C isotopic ratio, and 15-N/14-N isotopic ratio. Two hundred ninety fish samples were analyzed for total mercury, methylmercury, 13-C/12-C isotopic ratio, 15-N/14-N isotopic ratio, and total mass carbon and nitrogen. Water-quality field measurements made with a multi-parameter sonde included water temperature, barometric pressure, specific conductance, dissolved oxygen, pH, and turbidity. The within-reservoir data includes seven data tables given as both machine readable tab-delimited text (*.txt) and Excel formats (*.xlsx): 1) DataDictionary_LCR17-21, the data dictionary, which provides definitions and details related to the six other data tables, and includes citations of analytical methods; 2) SurfWater_Field-Lab_LCR17-20, the surface water and bottom water data table; 3) Sediment_LCR17-20; 4) PoreWater_LCR17-20; 5) Zooplankton_LCR17-20; 6) Fish_LCR18-21; and 7) SurfWater_Profiles_LCR17-20.

This dataset includes field measurements and laboratory analyses of surface water, bottom water (sediment-water interface), surficial (0-2 cm) sediment, pore water (0-2 cm), and biota collected in Lake Combie, California, from September 2017 through August 2021. The study area includes six sites within the reservoir where discrete samples of surface water, bottom water, sediment, and pore water were taken along the length of the reservoir at the following distances from the spillway: 0.07 miles, 0.5 miles, 0.9 miles, 1.2 miles, 1.3 miles, and 1.4 miles. The within-reservoir sites were sampled during September 2017, February 2018, and May 2018, prior to a large sediment removal operation, and again during September 2019, February 2020, and June 2020 following the removal operation. Zooplankton samples were collected at four of the six sites during the sampling period. Fish were collected from within two regions of the lake: in the Wooley Creek arm of the lower reservoir, and in the upper reservoir near the targeted area for sediment removal operations. Vertical profiles of water quality were measured with a multi-parameter sonde during water collection events and during one zooplankton event. Thirty-six surface water and thirty-six bottom water samples were collected at each site and analyzed for total mercury (filtered and particulate), methylmercury (filtered and particulate), total suspended solids, sulfate, chloride, selected dissolved nutrients, particulate 13-C/12-C and 15-N/14-N isotopic ratios, total particulate carbon and nitrogen, particulate carbon to nitrogen molar ratio, dissolved organic carbon, and dissolved organic-matter properties (absorption and fluorescence). Thirty-six bed-sediment samples were analyzed for total mercury, methylmercury, total reduced sulfur, and organic content. Pore water extracted from bed sediment was analyzed for filtered total mercury, filtered methylmercury, sulfate, chloride, selected dissolved nutrients, and dissolved organic carbon. Surface water, bottom water, and sediment collections included an additional four field replicates each for analysis - pore water had six replicates. One hundred six zooplankton samples and twenty-three replicates were analyzed for total mercury, methylmercury, 13-C/12-C isotopic ratio, and 15-N/14-N isotopic ratio. Two hundred ninety fish samples were analyzed for total mercury, methylmercury, 13-C/12-C isotopic ratio, 15-N/14-N isotopic ratio, and total mass carbon and nitrogen. Water-quality field measurements made with a multi-parameter sonde included water temperature, barometric pressure, specific conductance, dissolved oxygen, pH, and turbidity. The within-reservoir data includes seven data tables given as both machine readable tab-delimited text (*.txt) and Excel formats (*.xlsx): 1) DataDictionary_LCR17-21, the data dictionary, which provides definitions and details related to the six other data tables, and includes citations of analytical methods; 2) SurfWater_Field-Lab_LCR17-20, the surface water and bottom water data table; 3) Sediment_LCR17-20; 4) PoreWater_LCR17-20; 5) Zooplankton_LCR17-20; 6) Fish_LCR18-21; and 7) SurfWater_Profiles_LCR17-20.