Abstract Freshwater habitats are vital for both humans and nature owing to their exceptional biodiversity and valuable ecosystem services, but they are currently facing serious threats. The designation and management of protected areas have been proposed as the most feasible way to ensure conservation objectives for the future. However, traditional approaches have not protected freshwater fauna effectively, especially freshwater fish. Previous studies have identified the most irreplaceable terrestrial places to achieve conservation goals. Here, the aim was to investigate how the present network of protected areas preserves irreplaceable rivers for freshwater fish. The irreplaceability of the world's river basins was calculated using International Union for the Conservation of Nature Red List distribution maps, considering the rarity, richness, and conservation status of their freshwater fish fauna. The overlap between irreplaceable basins and the present network of protected areas was also calculated. The results highlight the conservation significance of tropical rivers, particularly those in the Neotropics. The subset of the basins covering 30% of the most irreplaceable land surface (in line with the United Nations 30by30 target) encompasses 99% of freshwater fish species. However, protected areas do not seem to provide sufficient protection to these basins, as 89% of their surface area lies outside protected areas. Only 7% of freshwater ecoregions meet the United Nations 30by30 target. Given the context of climate change, allocating new protected areas becomes crucial in providing better survival opportunities for freshwater fish species. Despite the limitations inherent to the absence of total knowledge of freshwater fish biogeography and the irreplaceability index itself, this study identifies priority sites for their conservation that may help inform decision‐making in the future to establish more effective protected areas.