Fishes in Mediterranean climates are adapted to thrive in streams with dynamic environmental conditions such as strong seasonality in flows. However, anthropogenic threats to species viability, in combination with climate change, can alter habitats beyond native species environmental tolerances and may result in extirpation. Although the effects of a Mediterranean climate on aquatic habitats in California have resulted in a diverse fish fauna, freshwater fishes are significantly threatened by alien species invasions, the presence of dams, and water withdrawals associated with agricultural and urban use. A long history of habitat degradation and dependence of salmonid taxa on hatchery supplementation are also contributing to the decline of fishes in the state. These threats are exacerbated by climate change, which is also reducing suitable habitats through increases in temperatures and changes to flow regimes. Approximately 80% of freshwater fishes are now facing extinction in the next 100 years, unless current trends are reversed by active conservation. Here, we review threats to California freshwater fishes and update a five-tiered approach to preserve aquatic biodiversity in California, with emphasis on fish species diversity. Central to the approach are management actions that address conservation at different scales, from single taxon and species assemblages to Aquatic Diversity Management Areas, watersheds, and bioregions.