Monitoring and Modeling of Nutrients and Other Water-Quality Constituents in Tributaries to Clear Lake, California
Clear Lake, the largest natural lake entirely within California, has a severe problem with harmful algal blooms (HABs). HABs can be detrimental to aquatic life because when the algae dies, sinks, and decays, the lake is deprived of the dissolved oxygen that fish need to breathe. A driving factor of these conditions are the nutrient loads being carried into the lake by soil erosion and the transport of sediment from the lake’s tributaries. The recent increase in wildfire size and frequency may also be a contributing factor to additional nutrients being introduced into the lake.

In addition to nutrients, Clear Lake has high levels of mercury due to the presence of an inactive mercury mine located on the lake’s southeast shores. Previous work at Clear Lake has shown that the increased algae growth, by depleting oxygen upon its decay, is a key driver to methylation of mercury, further impacting the lake’s food web and ecosystem.
Objective
This study is focused on the quantifying the contributions of nutrients and mercury into Clear Lake from its tributaries. Understanding the amounts of these constituents coming from the lake’s watershed is essential for effective remediation (restoration) through implementation of best management practices. The data collected from this monitoring effort will be used to determine the effectiveness of remediation actions and to calibrate watershed models.
The study’s objectives are to complete watershed monitoring to support two models to be developed by USGS. A sediment fingerprinting study will be conducted to help determine sources of sediment, total nitrogen, and total phosphorus in tributary streams that drain into Clear Lake, and to support collaborative nutrient and mercury modeling efforts with UC Davis.

Approach
The work is divided into tasks under two separate headings: Monitoring and Modeling.
Monitoring
The monitoring program includes the construction, operation, and maintenance of four new gaging stations in tributaries to Clear Lake. In addition to continuous data for flow, turbidity, and water temperature to be collected at the four gaging stations, at these and other stations, water samples will be collected and analyzed for nitrogen, phosphorus, and suspended sediment; mercury and methylmercury will be analyzed at selected locations (see map).
Monitoring tasks
- Construction, operation, and maintenance of four new gaging stations in tributaries to Clear Lake
- Tributary monitoring for water quality
Modeling
Results from the monitoring will be used as a basis for watershed modeling. The objective of the modeling component is to develop a quantitative understanding of sediment, nutrient, and mercury sources within the watershed so that best management practices can be most effectively applied to reducing loads of key constituents that adversely affect water quality in Clear Lake.
Modeling Tasks
- Project Management and Outreach
- Sediment Fingerprinting
- HSPF modeling of flow, sediment, and nutrient transport with climate-change scenarios
- SPARROW modeling of nutrients and sediment loads and sources
- A visualization and mapping tool showing results of models
Anticipated Products
Three interpretive reports are planned, describing results from HSPF, SPARROW, and sediment fingerprinting. USGS data releases (in ScienceBase) will be published as needed to support the interpretive reports.
Mercury studies at Sulphur Bank Mercury Mine and Clear Lake, California
Hydrologic and Aquatic Ecology Studies at Clear Lake, California
Scotts Creek Nutrient Erosion Study, Lake County, California
Effects of Wildfire and Fire Retardants on Nutrient Transport in California Watersheds
Water Quality Vertical Profiles in Clear Lake, Lake County, California, 2017-2023 (ver. 4.0, May 31, 2024)
Mapping watershed potential to contribute phosphorus from geologic materials to receiving streams, southeastern United States
Trends in nitrogen, phosphorus, and sediment concentrations and loads in streams draining to Lake Tahoe, California, Nevada, USA
Spatially referenced models of streamflow and nitrogen, phosphorus, and suspended-sediment loads in streams of the Pacific region of the United States
Sediment Source Assessment Using Sediment Fingerprints
Sediment fingerprinting to delineate sources of sediment in the agricultural and forested Smith Creek Watershed, Virginia, USA
Determining the sources of fine-grained sediment using the Sediment Source Assessment Tool (Sed_SAT)
Characterizing changes in streamflow and sediment supply in the Sacramento River Basin, California, using hydrological simulation program—FORTRAN (HSPF)
Sources and transport of phosphorus to rivers in California and adjacent states, U.S., as determined by SPARROW modeling
SPARROW modeling of nitrogen sources and transport in rivers and streams of California and adjacent states, U.S.
Downscaling future climate scenarios to fine scales for hydrologic and ecological modeling and analysis
Watershed Monitoring in Clear Lake Tributaries
Clear Lake, the largest natural lake entirely within California, has a severe problem with harmful algal blooms (HABs). HABs can be detrimental to aquatic life because when the algae dies, sinks, and decays, the lake is deprived of the dissolved oxygen that fish need to breathe. A driving factor of these conditions are the nutrient loads being carried into the lake by soil erosion and the transport of sediment from the lake’s tributaries. The recent increase in wildfire size and frequency may also be a contributing factor to additional nutrients being introduced into the lake.

In addition to nutrients, Clear Lake has high levels of mercury due to the presence of an inactive mercury mine located on the lake’s southeast shores. Previous work at Clear Lake has shown that the increased algae growth, by depleting oxygen upon its decay, is a key driver to methylation of mercury, further impacting the lake’s food web and ecosystem.
Objective
This study is focused on the quantifying the contributions of nutrients and mercury into Clear Lake from its tributaries. Understanding the amounts of these constituents coming from the lake’s watershed is essential for effective remediation (restoration) through implementation of best management practices. The data collected from this monitoring effort will be used to determine the effectiveness of remediation actions and to calibrate watershed models.
The study’s objectives are to complete watershed monitoring to support two models to be developed by USGS. A sediment fingerprinting study will be conducted to help determine sources of sediment, total nitrogen, and total phosphorus in tributary streams that drain into Clear Lake, and to support collaborative nutrient and mercury modeling efforts with UC Davis.

Approach
The work is divided into tasks under two separate headings: Monitoring and Modeling.
Monitoring
The monitoring program includes the construction, operation, and maintenance of four new gaging stations in tributaries to Clear Lake. In addition to continuous data for flow, turbidity, and water temperature to be collected at the four gaging stations, at these and other stations, water samples will be collected and analyzed for nitrogen, phosphorus, and suspended sediment; mercury and methylmercury will be analyzed at selected locations (see map).
Monitoring tasks
- Construction, operation, and maintenance of four new gaging stations in tributaries to Clear Lake
- Tributary monitoring for water quality
Modeling
Results from the monitoring will be used as a basis for watershed modeling. The objective of the modeling component is to develop a quantitative understanding of sediment, nutrient, and mercury sources within the watershed so that best management practices can be most effectively applied to reducing loads of key constituents that adversely affect water quality in Clear Lake.
Modeling Tasks
- Project Management and Outreach
- Sediment Fingerprinting
- HSPF modeling of flow, sediment, and nutrient transport with climate-change scenarios
- SPARROW modeling of nutrients and sediment loads and sources
- A visualization and mapping tool showing results of models
Anticipated Products
Three interpretive reports are planned, describing results from HSPF, SPARROW, and sediment fingerprinting. USGS data releases (in ScienceBase) will be published as needed to support the interpretive reports.