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).