In-shore dolphins are potentially the most threatened of South American’s marine mammals because of their close proximity to human influences. South America is a global hotspot of marine mammal conservation but because of regional limitations, there is restricted on-the-ground information about the spatial distribution of cetaceans. To identify the species most at risk, we model the species distributions of five in-shore dolphin species; the Chilean, Comerson’s, dusky, Franciscana and Peale’s dolphins. To assess the main drivers of their distribution, we inferred species distribution models using spatial sighting data for eastern and western South America. We included six eco-geographical variables: bathymetry, habitat, sea surface temperature and distance to canyons, to the coast, and freshwater to assess the main drivers of spatial distribution. We also estimated the degree of spatial overlap between species and niche overlap models using the Schoener’s D Test. We found that the main drivers for species with reduced distribution are the distance to the coast and freshwater, whereas the drivers for the species with a wider distribution range are the distance to the coast and bathymetry. According to our distribution analysis, we identify that the in-shore dolphin species most vulnerable to anthropogenic impacts are the Chilean, Franciscana and Peale’s dolphins. Although many marine mammal species remain classified as data deficient under the International Union for Nature, our case study shows that SDMs together with historical distribution data and environmental variables, can be used to identify species most at risk, to target future research and management priorities.