The water quality of Clear Lake — California’s largest natural freshwater lake — suffers from low-to-no-oxygen conditions that contribute to harmful algal blooms (HABs) and other issues, according to a report from the UC Davis Tahoe Environmental Research Center and the U.S. Geological Survey.

Clear Lake has long suffered from environmental challenges associated with mercury contamination, high nutrient levels, low dissolved oxygen and HABs, which threaten aquatic and human health and the community’s cultural, recreational and economic activities. 

The report, submitted to the Blue Ribbon Committee for the Rehabilitation of Clear Lake, outlines the primary causes of deteriorating water conditions at the 63-square-mile lake. It also applies newly developed predictive tools to test restoration strategies and offers actionable recommendations. These include installing a hypolimnetic oxygenation system, a technology that has been used nationwide and in California to enhance oxygen levels at the lake bottom. 

Low-to-no-oxygen, or anoxic, conditions near the lake bottom are created by seasonal temperature stratification, where a warm layer of water on top of the lake prevents oxygen from reaching the bottom. 

“This anoxic bottom layer is triggering the bad mechanisms in the lake,” said Alicia Cortés, lead UC Davis TERC project scientist for the Clear Lake project. “These conditions cause lake sediments to release nutrients — particularly phosphorus — which can trigger adverse outcomes like HABs. Low oxygen may also harm fish habitat or produce methylmercury — a highly toxic form of mercury.”

To address these challenges, TERC recommends implementing hypolimnetic oxygenation systems. These systems aim to enhance oxygen levels in deeper waters to reduce the release of phosphorus from the sediments. This can potentially reduce HABs, enhance fish habitat, reduce methylmercury production and improve overall aquatic health. The report recommends the Oaks Arm, the smallest arm of the lake frequently affected by HABs and mercury contamination, as the installation site for a prototype system.

Monitoring Clear Lake

For the report, TERC researchers partnered with the USGS to conduct a multi-year study to understand the dominant processes in Clear Lake and its watershed that are diminishing water quality. 

“Clear Lake is highly dynamic, with strong currents that quickly move particles between its basins and frequent mixing events that alter the vertical distribution of temperature, oxygen, nutrients and harmful algal blooms,” said Alexander Forrest, interim director of TERC and a UC Davis professor in the department of Civil and Environmental Engineering. “These water movements need to be accounted for to make any rehabilitation strategy feasible and sustainable in the long run.”

To understand these complexities, TERC researchers developed a continuous and multidisciplinary monitoring program, with measurements collected every hour for five years. Researchers installed sensors to track water temperatures, oxygen levels and real-time meteorological conditions. TERC researchers also collected hundreds of water samples to quantify nutrients and phytoplankton concentrations, including HABs, and created a high-resolution bathymetry map of the lake bottom. 

Researchers at USGS quantified nutrient and sediment loads entering the lake from the watershed via streams. This is a crucial component of understanding the full system that can influence water quality.

These on-site measurements were essential to developing predictive models for Clear Lake and its watershed. These models help reveal the processes degrading water quality. They show how the lake and watershed respond to changing environmental conditions and future restoration strategies, and they help inform management.

Clear Lake support

TERC received a $1.1 million grant from the California Natural Resources Agency to support the planning and permitting phase for a prototype of the hypolimnetic oxygenation system and for community outreach. This funding will also support real-time, on-site dissolved oxygen measurements near the lake bottom in the Oaks Arm. 

The 15-member Blue Ribbon Committee for the Rehabilitation of Clear Lake was created by state legislation in 2017 to propose effective solutions to the decline of water quality at the lake. It includes representatives from local Indigenous tribes, Lake County, UC Davis and the Central Valley Regional Water Quality Control Board. Four members appointed by Lake County have expertise in agriculture, economics, environment and public water supplies.

The UC Davis Tahoe Environmental Research Center remains dedicated to conducting rigorous research and fostering environmental stewardship of California's prized natural resources. Through continued collaboration and innovation, TERC envisions a future where Clear Lake thrives again.