Detailed knowledge on habitat use by marine mammals is critical for understanding their ecological role and for adequate management. Here, we assess the habitat use patterns of thirteen species of marine mammals along the salinity gradient of the Río de la Plata estuary and the adjoining western South Atlantic Ocean, for which we use the ratios of stable oxygen isotopes in bone carbonate (apatite) as a proxy for salinity. Furthermore, we compare the results with those found from analysing the distance of the stranding site from the innermost point of the estuary. The overall evidence indicates that stable oxygen isotopes can be good tracers of habitat use, as they distinguish those species that regularly use inshore estuarine-coastal ecosystems from those that are restricted to offshore pelagic oceanic waters. In contrast, sampling location does not sufficiently characterize the species’ habitat, since other factors can be involved in the animals being transported to stranding sites far from their typical habitats. In conclusion, the analysis of stable oxygen isotopes represents a useful and inexpensive approach to studying habitat use among marine mammals where salinity gradients exist.