The herpetofauna of north-west Africa includes four species of semi-aquatic reptiles. In north-west Africa, Emys orbicularis and Natrix astreptophora are stenotopic species having fragmented distributions, while Mauremys leprosa and Natrix maura occur throughout the region (eurytopic species). We investigated the factors underlying these distributional patterns and tested the hypothesis that species sharing similar resources tend to be spatially segregated. We characterized the niches of the species based on climatic, topographic, soil texture, landscape and hydrological predictors. The relationship between the presence of a species and the environmental gradient was assessed using distance-based linear models, and habitat suitability was modelled using Random Forests. Our results indicated that both E. orbicularis and N. astreptophora occupy extreme positions within the environmental gradient. Climate and landscape were the major factors influencing the relative occurrences of the stenotopic and eurytopic species. However, these semi-aquatic reptiles are likely to be subject to similar ecological constraints, as their occurrence was positively associated with greater complexity of the drainage system. Thus, there was a high degree of niche overlap between the stenotopic and eurytopic species at large spatial scales.