Efforts to set global conservation priorities have largely ignored freshwater diversity, thereby excluding some of the world's most speciose, threatened, and valuable taxa. Using a new global map of freshwater ecoregions and distribution data for about 13,300 fish species, we identify regions of exceptional freshwater biodiversity and assess their overlap with regions of equivalent terrestrial importance. Overlap is greatest in the tropics and is higher than expected by chance. These high-congruence areas offer opportunities for integrated conservation efforts, which could be of particular value when economic conditions force conservation organizations to narrow their focus. Areas of low overlap—missed by current terrestrially based priority schemes—merit independent freshwater conservation efforts. These results provide new information to conservation investors setting priorities at global or regional scales and argue for a potential reallocation of future resources to achieve representation of overlooked biomes.