Fossil diatoms from a 177-m core (CL-80-1) taken near the center of the main basin (Upper Arm) of Clear Lake, California, provide evidence about the stratigraphie relationships, age, and environmental history of these lacustrine deposits. In general, diatom assemblages from the core are dominated by planktonic genera such as Stephanodiscus, Cyclotella, and Melosira. Shallow-water species of Fragilariaand Amphoraare common and sometimes abundant. Several planktonic diatoms from the core are also found in the Kelseyville Formation, which is exposed on the southern margin of Clear Lake and is inferred to underlie the modern lacustrine deposits. The presence of these taxa in the same stratigraphie order in both the Clear Lake core and the Kelseyville Formation suggests partial correlation between the two and implies a relationship between the Kelseyville Formation and the lacustrine sediments beneath Clear Lake.

In the upper 50 m of core CL-80-1, diatom assemblages apparently reflect late Pleistocene and Holocene paleoenvironmental changes, although their environmental significance may be obscured by reworking of diatoms from older sediments, by tectonically caused changes in patterns and rates of sedimentation, and by the impact of volcanism. Nevertheless, the diatoms indicate that lacustrine environments have been characterized by fresh, moderately deep, nutrient-rich water throughout much of their sedimentary history. Cooler climatic and lacustrine environments of the late Pleistocene were characterized by a codominance of Stephanodiscusand Melosiraspecies, implying a mesotrophic to eutrophic, stratified lake. After the change from Pleistocene to Holocene climates, Clear Lake became yet more eutrophic and turbid. Stratification was short-term and irregular, and warm-water conditions extended throughout a greater portion of the growing season although there is evidence for a middle Holocene return to cooler and moister conditions.

The modern limnology of Clear Lake, which is characterized by massive blooms of blue-green algae and by the abundance of Melosira granulata, apparently began about 15,000 years ago.