Degradation of freshwater ecosystems is a global crisis best understood through intensive study of well-studied regional faunas. A quantitative protocol was used to determine conservation status of all 129 freshwater fishes native to California. Seven (5%) are extinct; 34 (26%) qualified for listing as endangered or threatened species; 32 (25%) were rated as imperiled, qualifying as California Species of Special Concern, with potential for listing; 34 (26%) rated being on a watch list and 22 (17%) were found to be relatively secure. Of 31 species officially listed under federal and state endangered species acts, 17 (55%) clearly qualified for listing under our criteria and 12 (39%) were rated as species of special concern. Conversely, of 34 extant species with the lowest ratings under our criteria, only 17 (50%) were officially listed. Climate change, area occupied and anthropogenic threats had the largest negative impact on status. Of the 15 categories of anthropogenic threats analyzed, those most likely to diminish status were alien species, agriculture and dams. Overall, 83% of California’s freshwater fishes are extinct, endangered, or in decline, a 16% increase since 1995 and a 21% increase since 1989. The decline seen in California’s inland fishes is probably typical of declines in areas that are less well documented, indicating a strong need for better methods of conservation of freshwater ecosystems.