Globally, freshwater species are under threat from human mediated stressors. Therefore, there is an urgent need for methods to estimate population and species occurrences for conservation purposes. Here, we used a predictive species distribution model to determine the occurrence of three endangered species (Amietia inyangae, Chlorolestes elegans and Strongylopus rhodesianus) in Southern Africa (Eastern Highlands of Zimbabwe). The study revealed that the probability of occurrences for the three species increase with an increase in elevation and annual precipitation and decrease with an increase in annual mean temperature. Our results indicated that the highest probability of occurrences for A. inyange, C. elegans and S. rhodesianus is in the Nyanga, Stapleford and Chimanimani highland areas, with some probabilities of occurrence falling outside protected areas. Our findings suggest that the areas covered by protected areas may need to be revaluated. Our findings will be useful for managing threatened species.