Bottlenose dolphins (Tursiops truncatus) and pantropical spotted dolphins (Stenella attenuata) co-occur in Golfo Dulce, a fjord-like embayment located in the southern Pacific coast of Costa Rica. We evaluated if spatial overlap by these dolphin species is associated with similar environmental requirements. Presence-only models based on niche theory were constructed by contrasting a set of spatial locations with the responses of the target species to abiotic ecogeographical variables (EGVs: depth, slope, distance to rivers, distance to 200 m isobath, mean sea surface temperature, and variation in sea surface temperature). Models were cross-validated with levels of discrimination that ranged from acceptable to excellent based on the area under the curve assessment (T. truncatus, rainy season: 0.76, dry season: 0.83; S. attenuata, rainy season: 0.84, dry season: 0.89). Both dolphin species occur in Golfo Dulce year-round; the lack of seasonality documented previously was supported by the models. Species distribution models showed no spatial overlap, with differences in EGVs affecting their distribution (T. truncatus: distance to river distance to 200 m isobath, S. attenuata: depth sea surface temperature). We argue that the coexistence of both predators in Golfo Dulce is linked to habitat heterogeneity, where critical habitats are spatially differentiated. The lack of fine-scale spatial overlap, along with influential abiotic variables, highlights a process of coexistence for dolphins that are sympatric at the scale of Golfo Dulce, but within the Gulf there is fine-scale allopatry.