This study investigated whether there is evidence of widespread niche partitioning based on environmental factors in the Black Sea and tested the hypothesis that physiographic factors may be employed as predictors. It addresses poorly researched areas with good habitat potential for the only three cetacean subspecies living in this area: the Black Sea short-beaked common dolphin (Delphinus delphis spp. ponticus), the Black Sea bottlenose dolphin (Tursiops truncatus spp. ponticus) and the Black Sea harbour porpoise (Phocoena phocoena spp. relicta). Generalized additive models (GAMs) were used to analyse data collected from multiple sources. In total, 745 sightings of the three species between 1998 and 2010 throughout the Black Sea were included. The analysis found depth and sea surface temperature to be the most important variables for separating the occurrence of the three species. Common dolphins occurred mainly in deep waters and in areas where the sea surface temperature was low, bottlenose dolphins were distributed primarily in shallower and warmer waters than common dolphins, and harbour porpoises were distributed in shallower waters with lower sea surface temperature than bottlenose dolphins. This study suggests strong niche segregation among the three cetacean species. The study is also the first contribution to the basic information of cetacean species distribution and habitat preferences in the Black Sea as a whole. Knowledge of the distribution of the three dolphin species in the study area is essential to establish conservation measures for these populations.