ABSTRACT: Deep scattering layers (DSLs) play an important role in pelagic food webs, serving as a vehicle for transferring energy between productive surface waters and the deep sea. We explored the spatial dynamics of DSLs off the Bahamas in shaping oligotrophic ecosystems. We compared 2 areas known to be important foraging habitats for a deep-diving predator, Blainville’s beaked whales: the Tongue of the Ocean (TOTO), an oceanographically isolated habitat, and the waters off Abaco Island, an oceanographically connected habitat. Using ship-based multifrequency echosounders and direct net sampling, we identified common layer structures characterized by diffuse, broad layers (>100 m in thickness) observed across the study areas. Within those diffuse layers, we occasionally observed distinctively bounded intense layers (~20 m in thickness) located at the upper edges of the DSLs. We found that spatial variability of layer structures shaped the Bahamian ecosystem. By comparing common layer types across the sampling locations, 2 potential mechanisms were identified. The area off Abaco Island was characterized by diffuse layers comprised of larger animals with greater migration distance and biomass than the habitat in TOTO, suggesting that Abaco may transfer more energy between energy-rich surface waters and the deep sea. Within TOTO, habitat most frequently used by beaked whales was characterized by the highest occurrence of intense layers dominated by thinner layers, suggesting such fine-scale structures may increase foraging efficiency by layer predators. Spatial variability of the DSL structures reveals the dynamics of the Bahamian mesopelagic ecosystem, potentially driving the beaked whales through bottom-up control of their prey.