The Sulphur Bank Mercury Mine (SBMM), active intermittently from 1873–1957 and now a USEPA Superfund site, was previously estimated to have contributed at least 100 metric tons (10⁵ kg) of mercury (Hg) into the Clear Lake aquatic ecosystem. We have confirmed this minimum estimate. To better quantify the contribution of the mine in relation to other sources of Hg loading into Clear Lake and provide data that might help reduce that loading, we analyzed Inputs and Outputs of Hg to Clear Lake and Storage of Hg in lakebed sediments using a mass balance approach. We evaluated Inputs from (1) wet and dry atmospheric deposition from both global/regional and local sources, (2) watershed tributaries, (3) groundwater inflows, (4) lakebed springs and (5) the mine. Outputs were quantified from (1) efflux (volatilization) of Hg from the lake surface to the atmosphere, (2) municipal and agricultural water diversions, (3) losses from out-flowing drainage of Cache Creek that feeds into the California Central Valley and (4) biotic Hg removal by humans and wildlife. Storage estimates include (1) sediment burial from historic and prehistoric periods (over the past 150–3,000 years) from sediment cores to ca. 2.5m depth dated using dichloro diphenyl dichloroethane (DDD), ²¹⁰Pb and ¹⁴C and (2) recent Hg deposition in surficial sediments. Surficial sediments collected in October 2003 (11 years after mine site remediation) indicate no reduction (but a possible increase) in sediment Hg concentrations over that time and suggest that remediation has not significantly reduced overall Hg loading to the lake. Currently, the mine is believed to contribute ca. 322–331 kg of Hg annually to Clear Lake, which represents ca. 86–99% of the total Hg loading to the lake. We estimate that natural sedimentation would cover the existing contaminated sediments within ca. 150–300 years.