Getting to the Bottom of What Fuels Algal Blooms in Clear Lake

By: Nick Framsted

Clear Lake is one of California’s oldest and most unique natural features. Nestled in Northern California’s coastal mountains, Clear Lake is the largest lake completely within California and is the oldest lake in North America with sediments dating back 480,000 years (Sims et al. 1988). Rich mineral deposits around the lake were historically mined for borax, sulphur, and mercury. Thus, Clear Lake continues to be polluted by mercury and methylmercury which bioaccumulates in the food chain (Suchanek et al. 2008). In spite of pollution, the lake boasts an impressive diversity of biological life. It is designated as an Important Bird Area by the Audubon Society, and has endemic species such as the Clear Lake hitch (Lavinia exilicauda chi, a planktivorous fish), the Clear Lake splittail (Pogonichthys ciscoides, now extinct), and Clear Lake gnat (Chaoborus astictopus)—the latter of which was targeted by heavy application of of the pesticide DDD to control large swarms (Lindquist et al. 1951). These pesticide applications earned Clear Lake a feature in Rachel Carson’s seminal novel Silent Spring for its negative impacts on Western Grebe populations.

Water Quality Issues in Clear Lake

Fig. 1. Operating a steam shovel to mine mercury, or quicksilver as it was called at the time, from a sulphur bank near Clear Lake. Photo from Anderson 1936.

Clear Lake continues to struggle with long-lasting impacts of nutrient pollution. High concentrations of nutrients such as nitrogen and phosphorus fuel large algal blooms and contribute to poor water quality in the lake. Phosphorus is particularly abundant in Clear Lake and its associated watershed. As a result, harmful phytoplankton known as cyanobacteria thrive here, some of which can produce toxins harmful to humans. Commonly known as blue-green algae, cyanobacteria are an ancient group of organisms that are actually unrelated to algae since they are considered bacteria and not plants. Perhaps the most important difference between cyanobacteria and algae is that some species of cyanobacteria have specialized cells called heterocysts that capture nitrogen gas from the atmosphere and transform it into usable forms through a process called nitrogen fixation–something that plants are not capable of. In fact, legumes like soybeans and clover actually have symbiotic relationships with other nitrogen-fixing bacteria in order to glean nitrogen for their own use. 

Fig. 2. Cyanobacterial bloom in the Oaks Arm of Clear Lake, CA in 2016. Photo courtesy of Holly Harris.

Nitrogen fixation gives cyanobacteria a competitive advantage in waters rich in phosphorus and relatively deficient in nitrogen–the exact conditions present in Clear Lake. Cyanobacteria thrive in Clear Lake and often form harmful algal blooms, or HABs, which are both ecologically damaging and dangerous to human health. In an effort to promote public safety, the Big Valley Band of Pomo Indians and the Elem Indian Colony collaboratively established an extensive cyanobacterial monitoring program to inform the public about current cyanotoxin levels around the lake. Annually, Clear Lake suffers major economic losses stemming from HABs, and a 1994 study estimated Lake County loses $7-10 million in tourist revenue annually due to HABs (Goldstein & Tolsdorf 1994). This value likely underestimates current tourism losses over 20 years later, and maintaining the economic viability of Clear Lake is paramount since it is located in the poorest county in the state. 

Restoring a Naturally Eutrophic Lake

Even before human settlement, Clear Lake was historically a productive lake due to phosphorus-rich rocks and sediments in the area (Bradbury 1988; Richerson et al. 2008). Eutrophic, or nutrient-rich lakes, do not inherently have poor water quality, despite their negative connotations. Clear Lake existed as a healthy, productive ecosystem for many thousands of years before European colonization. Algae forms the base of lake foodwebs, and algal abundances in Clear Lake create conditions that support trophy largemouth bass populations at higher densities than most other lakes.

Despite some ecological benefits of algae, there comes a point where too much becomes harmful. At high enough levels, massive algal blooms ultimately die and biodegrade. This dynamic ultimately depletes dissolved oxygen and robs waterbodies of vast swaths of habitat for fish and aquatic life. Such conditions contribute to fish kills, especially during increasingly prolonged bouts of hot temperatures (Till et al. 2019). In order to maintain suitable dissolved oxygen levels, nutrient levels must be managed to prevent large algal blooms. Therefore, efforts to restore Clear Lake have focused on identifying and managing phosphorus sources to curb their harmful effects. 

Phosphorus from the Deep: Internal Loading

Clear Lake has two main phosphorus sources: the surrounding watershed, and lake sediments, or muck, at the bottom of the lake. This muck consists of terrestrial particles that get washed into the lake and dead organisms that sink down and accumulate over time—just like dust settling on an old shelf. The resulting layer of sediment is densely packed with phosphorus and prone to releasing it to the lake during periods of low dissolved oxygen, or hypoxia, near the lake-bottom. When this occurs, lake sediments fertilize the lake and cause harmful algae blooms. This process is called internal loading, and it has been one of the main focuses of the UC Davis Tahoe Environmental Research Center’s (TERC) research in Clear Lake. With the help of the Lake County Water Resources Department and their long-term dataset on sediment-associated phosphorus, our team has been working to track how sediment phosphorus levels have changed over time.

Predicting Hypoxia and Internal Loading in Clear Lake

Fig. 3. Collecting intact sediment cores from the bottom of Clear Lake (left image) to investigate rates of phosphorus flux from sediments using incubations (middle and right images). Photos: Micah Swann.

We have taken a multi-pronged approach to estimating impacts of internal loading to Clear Lake. Since phosphorus only mobilizes from sediments during hypoxic conditions, TERC scientist Alicia Cortes has been leading an effort to develop a hydrodynamic model to predict hypoxia throughout the lake using simple meteorological data, temperature sensors, and dissolved oxygen sensors at sites across the lake (Cortes et al. in prep). Using phosphorus flux rates measured from incubations of intact sediment cores, this model will help estimate annual internal loads of phosphorus to the lake. Preliminary research indicates that internal loading accounts for nearly half of phosphorus inputs to the lake annually.

Fig. 4. Soluble reactive phosphorus (phosphate) flux in anoxic sediment cores sampled from 6 sites across Clear Lake, CA. Sites show significant spatial variability in phosphorus flux indicating “hot spots” of internal loading exist across the lake.

The UC Davis team is working with outside organizations to identify and test management solutions to control internal phosphorus loading that are both economical and environmentally responsible. Our goal is to inform the Blue Ribbon Committee – a committee of local stakeholders in Lake County, on adjusting existing total maximum daily limits on phosphorus loads entering the lake and recommend strategies for managing internal phosphorus loads.

Questions? Feel free to visit our website

Nick Framsted is a masters student in the Department of Environmental Science and Policy at the University of California, Davis and the UC Davis Tahoe Environmental Research Center.

Further Reading

Anderson, C. A. (1936). Volcanic history of the Clear Lake area, California. Bulletin of the Geological Society of America, 47(5), 629-664.

Bradbury, J. P. (1988). Diatom biostratigraphy and the paleolimnology of Clear Lake, Lake County, California. Late Quaternary Climate, Tectonism, Sedimentation in Clear Lake, Northern California Coasts. Geological Society of America, Boulder CO. 1988. p 97-129.

Goldstein, J. J., & Tolsdorf, T. N. (1994). An Economic Analysis of Potential Water Quality Improvement in Clear Lake: Benefits and Costs of Sediment Control, Including a Geological Assessment of Potential Sediment Control Levels: Clear Lake Basin, Lake County, California. US Department of Agriculture, Soil Conservation Service, Davis and Lakeport Offices.

Lindquist, A. W., Roth, A. R., & Walker, J. R. (1951). Control of the Clear Lake Gnat in California. Journal of Economic Entomology, 44(4).

Richerson, P. J., Suchanek, T. H., Zierenberg, R. A., Osleger, D. A., Heyvaert, A. C., Slotton, D. G., … & Vaughn, C. E. (2008). Anthropogenic stressors and changes in the Clear Lake ecosystem as recorded in sediment cores. Ecological Applications, 18(sp8), A257-A283.

Sims, J. D. (Ed.). (1988). Late Quaternary Climate, Tectonism, and  Sedimentation in Clear Lake, Northern California Coast Ranges (Vol. 214). Geological Society of America.

Suchanek, T. H., Eagles-Smith, C. A., Slotton, D. G., Harner, E. J., & Adam, D. P. (2008). Mercury in abiotic matrices of Clear Lake, California: human health and ecotoxicological implications. Ecological Applications, 18(sp8), A128-A157.

Till, A., Rypel, A. L., Bray, A., & Fey, S. B. (2019). Fish die-offs are concurrent with thermal extremes in north temperate lakes. Nature Climate Change, 9(8), 637-641.

About Andrew Rypel

Andrew L. Rypel is a Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Director of the Center for Watershed Sciences.
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1 Response to Getting to the Bottom of What Fuels Algal Blooms in Clear Lake

  1. Denise "Dee Dee" Smart says:

    Could simple aeration of the lake have a positive impact?
    It occurs to me that perhaps by designing and engineering
    an aeration system specifically to address hypoxia in
    Clear Lake, we could once again begin to enjoy it’s natural
    beauty, and, of course the increased economic growth from
    tourism wouldn’t hurt…Thank you for your response.

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