Water-Quality Vertical Profiles in Clear Lake, Lake County, California

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 Sulphur 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 1990, the SBMM has been a Superfund site managed by the U.S. Environmental Protection Agency (EPA). 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 (2025) studies underway [collaborations between EPA, the U.S. Geological Survey (USGS), and  the University of California, Davis (UCD)] to improve the understanding of nutrient and mercury cycling within the lake. 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. The UCD part of the project is focused on developing a three-dimensional hydrodynamic computer model of the lake that simulates periodic stratification of temperature and dissolved oxygen, nutrient dynamics, and mercury cycling. The USGS part of the project is focused on monitoring of water quality conditions at locations in the lake and development of sensor-based methodologies for monitoring constituents of concern at relevant spatial and temporal scales. This approach requires 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, algal concentration, or fluorescent properties of dissolved organic matter).  The USGS data monitoring includes continuous data collected from moored sondes deployed at two sites, vertical profiles collected with sondes at multiple sites, and water quality samples collected at selected sites and depths. The vertical profiles collected with a YSI EXO2 multiparameter sonde is the subject of this data release.

This data release documents the results of water-quality vertical profiles during June 2020 through May 2025. It includes two 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 data table and includes citations of analytical methods; 2) T2_CL_Vertical_Profiles, the vertical profile surface-water dataset including water-quality parameters. Vertical profiles were collected at 17 sites in Clear Lake, with most sites profiled once or twice. Two of the sites in the Oaks arm have moored sondes collecting continuous data. Laboratory analytical results from water quality samples collected at selected depths in the vertical profiles are presented in Agee and others (2024). Additional vertical profiles have been collected by the USGS within Clear Lake in order to inform conservation and management decisions concerning the Clear Lake Hitch (Wulff and others, 2019).