This report provides a pre-historic and historic background from which to evaluate the importance and impacts of a multitude of natural and anthropogenic stresses imposed upon Clear Lake and its watershed. Specifically, we identify major geological, climatological, ecological, political, and economic factors that influence the outcome of management and policy level decisions on the health and well-being of the entire ecosystem, especially the lake proper. Natural stressors include: geologic and tectonic events, regional and global climate change, fires, droughts and floods. Anthropogenic stressors include: (1) modifications to the landscape - including fires, logging and deforestation, dam construction, and other creek modifications; (2) contaminants – including pesticides, mining, sewage and septic overflows; (3) land use changes, including original wetland losses (and some wet habitat increases – see above), dredging, filling and creek bed alterations, water table and shoreline modifications, road building, agriculture, soil exposure and transport, livestock grazing; and (4) species introductions including intentional and accidental introductions. Finally, we illustrate how scientific research has contributed significantly to addressing multiple management objectives in this extremely complex ecosystem.