Clear Lake Watershed and Lake Remediation: Final Report. University of California, Davis, prepared for State of California Natural Resources Agency, Grant GF2141-0

Clear Lake is a vital resource for water, recreation, and local Tribes, but it suffers from severe environmental impairments, including mercury contamination and frequent cyanobacterial harmful algal blooms (CHABs). The primary barrier to restoration has been a lack of quantitative data to predict how the lake responds to management actions. This joint project between the University of California, Davis Tahoe Environmental Research Center  (UCD-TERC) and the United States Geological Service (USGS), funded by the California Natural Resources Agency and endorsed by the Blue Ribbon Committee, aimed to develop a system-wide monitoring and modeling framework to identify the causes of poor water quality and evaluate potential remediation strategies. Extensive monitoring from 2019–2024 revealed that the root cause of Clear Lake’s water quality problems is seasonal hypoxia (low dissolved oxygen) near the lake bottom. This lack of oxygen triggers internal loading, where sediments release stored phosphorus (P) into the water column. Internal sources account for 70–95% of the total phosphorus input during the study period. While watershed runoff contributes nitrate in the winter/wet season, phosphorus concentrations in the summer are driven by sediment release when the creeks are dry. USGS monitoring identified Scotts Creek and Middle Creek as the largest contributors of sediment and nutrients. The project developed advanced predictive tools, including a 3D lake model coupled with watershed models, to simulate water quality responses. These models were used to virtually test pilot restoration strategies proposed by the Blue Ribbon Committee. The report concludes that restoration must focus on increasing dissolved oxygen at the lake bottom to control internal phosphorus loading on the seasonal scale, and address watershed sources by prioritizing erosion control in the upper Scotts Creek watershed and completing the Middle Creek wetland restoration to reduce agricultural nutrient loads on a decadal scale.