The status of freshwater fishes continues to decline despite substantial conservation efforts to reverse this trend and recover threatened and endangered aquatic species. Lack of success is partially due to working at smaller spatial scales and focusing on habitats and species that are already degraded. Protecting entire watersheds and aquatic communities, which we term "native fish conservation areas" (NFCAs), would complement existing conservation efforts by protecting intact aquatic communities while allowing compatible uses. Four critical elements need to be met within a NFCA: (1) maintain processes that create habitat complexity, diversity, and connectivity; (2) nurture all of the life history stages of the fishes being protected; (3) include a long-term enough watershed to provide long-term persistence of native fish populations; and (4) provide management that is sustainable over time. We describe how a network of protected watersheds could be created that would anchor aquatic conservation needs in river basins across the country.