Using photo-identification data, bottlenose dolphin (Tursiops truncatus) populations can be differentiated based on their use of particular estuaries or coastal habitats. Questions remain, however, about the validity of such fine-scale population partitioning and whether the resulting assemblages utilize unique forage bases. To address the issue of forage base use, stable isotopes of carbon (δ13C), nitrogen (δ15N) and sulfur (δ34S) were analyzed from skin tissues (n= 74) of bottlenose dolphins sampled seasonally along the coast and in three estuaries near Charleston, South Carolina. Autumn values of δ34S, δ15N, and δ13C and summer values of δ34S indicated that dolphins sampled from these four assemblages utilized unique forage bases, despite limited sample sizes. Likewise, autumn and spring differences in δ15N and δ13C values were evident in the North Edisto River, and in δ34S from dolphins sampled from all three estuarine assemblages; no seasonal differences were identified in the coastal assemblage. Results demonstrate the importance of considering spatial and temporal variation in forage base when developing local management plans for bottlenose dolphin and highlight the discriminatory power of δ34S for estuarine and coastal marine mammals. These results also suggest that stable isotopes could be developed as a complementary tool for photo-identification based partitioning of bottlenose dolphin populations.