1. Although freshwater ecosystems contain high biodiversity and provide valuable ecosystem services, they are severely threatened worldwide. Many broad-scale approaches to conserve freshwater environments have been proposed, but as headwaters tend to host higher levels of biodiversity, identifying priority areas for conservation at a local scale is essential.2. An integrative three-step framework is proposed to recognize such areas, using anomuran crabs of the family Aeglidae as biodiversity indicator taxa, within four freshwater ecoregions in South America. First, the knowledge on the distribution of species occurring within the study area was updated and the species conservation status assessed. Second, species distribution modelling was used to identify areas of high richness and endemism. Third, these areas were compared with the existing protected area network, in addition to land-use and urban information, to indicate priority areas for conservation within four freshwater ecoregions (Laguna dos Patos, Upper Uruguay, Lower Uruguay, Tramandaí and Mampituba) studied at a local scale.3. Analysis of the distribution of species of the genus Aegla showed that the present protected area network poorly covers freshwater habitats within the study region.Three priority areas for conservation were identified, with high levels of endemism and richness of aeglid species. These areas are mainly located close to current protected areas, and we suggest, therefore, that the enlargement of some protected areas, through the establishment of corridors, would better protect several species with distributions restricted to headwaters, such as macroinvertebrates and fishes, some of which are threatened with extinction.