The diversity and distribution of freshwater insects in South America is poorly known. Riffle beetles (Elmidae) are aquatic Coleoptera that are considered important indicators of environmental integrity. In Brazil, the country with the largest area and highest richness of Elmidae in the Neotropics, the diversity of the family remains incipient. The southern region of Brazil (state of Rio Grande do Sul) reportedly has a higher richness of stream insects than other regions. In this study, we used species distribution models (SDMs) to estimate the potential distribution of riffle beetle taxa in southern Brazil to identify areas with elevated diversity and suggest priority areas for further investigation towards conservation of Elmidae. As most records of Elmidae were represented by larvae, we predicted the potential distribution firstly of genera and secondly of species within the genus Macrelmis because they were available as adults and allowed identification to species level. These were modelled in relation to environmental factors such as climate, topography, hydrography and land cover. Our results suggested that montane regions and basins located within well-preserved forested regions indicated the highest potential richness of Elmidae. In addition, the areas with higher predicted suitability for the occurrence of genera overlapped with the suitable areas for species of Macrelmis. This result suggests the existence of an elevated ecological similarity among most of the modelled taxa, and that projections for certain Elmidae genera can be useful proxies for estimations of the potential distribution of species in the region. The most important environmental factors related to the predicted distribution of Elmidae taxa were associated with climate (precipitation), landscape (forest cover) and topography. Unsurprisingly, freshwater ecoregions were also suggested as important drivers of Elmidae distribution. Our results indicate that conservation efforts for aquatic insects such as riffle beetles in Brazil should focus on watersheds located in montane and forested regions.