Catchments of California’s Sierra Nevada have been managed for hydropower, water supply, recreation and the environment, during which regional freshwater ecosystems have experienced extirpations of anadromous fishes, widespread loss in amphibian abundance and increases in non-native species. California’s Mediterranean-montane climate is expected to warm by 2–6°C over the next century, reducing snowpack, causing earlier runoff and altering flows. Freshwater conservation efforts currently rely on a patchwork of legal and regulatory mechanisms, and have failed to achieve their full potential because of weak and uncoordinated implementation. No scheme adequately addresses freshwater conservation objectives such as representation and persistence, and all ignore anticipated impacts of climate change. We recommend that (1) existing legislation be fully implemented, with explicit anticipation of future conditions, (2) local institutions develop and implement a systematic freshwater conservation plan, focusing on resilience to climate warming, (3) policies be crafted to prioritise catchments to emphasise key regional objectives (e.g. conservation) and (4) regional planning agencies with regulatory authority be formed at the catchment level.