We employed numerical wave models, GIS, and stable isotope analyses of otolith material to identify interspecific differences in habitat and resource use among juveniles of two sympatric and morphologically indistinct bonefishes, A. goreensis and A. vulpes in littoral zones of The Bahamas. Both species occurred in similar water temperatures; however, A. goreensis juveniles occupied habitats characterized by greater wave-driven flow velocities and closer proximity to coral reefs than A. vulpes. Likewise, A. goreensis was present across a broader range of flow environments and sampling stations than A. vulpes, which was typically confined to sheltered, low-flow habitats. The results of stable isotope analyses were consistent with the species’ relationships with environmental parameters, providing support for differential habitat and/or resource utilization. Otolith δ18O did not differ significantly between species, suggesting they experience comparable thermal regimes. However, δ13C varied substantially, with the otoliths of A. goreensis depleted in 13C relative to A. vulpes by approximately 1‰, potentially signifying a greater reliance on pelagic carbon sources by the former, in agreement with observed distinctions in habitat use. In linear models, otolith δ13C was negatively correlated with ambient flow velocity and positively related to distance from coral reef habitats, and these relationships did not vary across species. After accounting for the effects of these variables, species-specific differences in otolith δ13C remained, indicating that other unknown factors contributed to the observed disparities. Collectively, our findings suggest that niche partitioning between A. goreensis and A. vulpes is likely mediated by their differential abilities to compete across various flow environments, likely as a result of divergent behavioral and/or physiological adaptation.