The Sierra Nevada, California’s iconic mountain range, harbors thousands of remote high-elevations lakes from which water flows to sustain agriculture and cities. As climate and air quality in the region change, so do the watershed processes upon which these lakes depend. In order to understand the future of California’s ecology and natural resources, we need an integrated account of the environmental processes that underlie these aquatic systems. Synthesizing over three decades of research on the lakes and watersheds of the Sierra Nevada, this book develops an integrated account of the hydrological and biogeochemical systems that sustain them. With a focus on Emerald Lake in Sequoia National Park, the book marshals long-term limnological and ecological data to provide a detailed and synthetic account, while also highlighting the vulnerability of Sierra lakes to changes in climate and atmospheric deposition. In so doing, it lays the scientific foundations for predicting and understanding how the lakes and watersheds will respond.