Modern-day Clear Lake is a turbulent, turbid, permanent, polymictic lake. It is also a highly productive fresh-water lake whose dominant solutes are Mg²⁺ + Ca²⁺ – HCO₃ ⁻. The lake has a diverse and abundant limnetic community, yet has a depauperate benthic community. The benthic community structure appears to be ecologically simple as the result of turbulence-induced substrate instability coupled with unpredictable periods of anoxia induced by the oxygen-consuming organic matter. Ostracodes, which are ubiquitous, largely benthic, environmentally sensitive, and diverse organisms, are represented in Clear Lake only by the nektic species Cypria ophtalmica. The substrate conditions provide adequate reason for the absence of most ostracodes from the modern lake, but their absence in the fossil record suggests that the modern lacustrine environment existed in the past despite known climate changes. This seeming paradox can be explained by considering the influence of various types of climatic change on the lacustrine environment; certain types of climate-environmental changes would maintain a lacustrine environment unsuited to ostracodes. These hypothesized climate-lacustrine environmental changes would favor the modern (Holocene) and other oak-dominated periods to be the warmest and driest in Clear Lake history, whereas the pine-TCT (Taxodiaceae, Cupressaceae, and Taxaceae) periods would be cooler and wetter than today. The largely barren ostracode record, coupled with rare ostracode occurrences, would support a glacial-interglacial Clear Lake climatic history characterized primarily by changes in the annual precipitation-evaporation budget.