Seventy-five surface (<4 cm) sediment samples were collected throughout Green Bay Cave System, Bermuda to investigate foraminiferal ecology and habitat variability in underwater coastal caves. This cave is ideal for studying different cave environments because it consists of an anchia-line cave environment connected to a submarine cave environment. Each sediment sample was analyzed for foraminifera, δ13Corg, C:N, organic matter content, CaCO3, and granulometry. Measurements of pH, salinity, dissolved oxygen, and temperature in the coastal aquifer distinguished the meteoric lens and saline groundwater. Q-mode cluster analysis on the foraminifera produced a dendrogram that segregates the anchialine and submarine cave environments, and subdivides each environment into distinct habitats consistent with local hydrogeology and sedimentology. The anchialine cave environment near the sinkhole is characterized by two groups of foraminifera: 1) the Meteoric Lens Assemblage living in the brackish meteoric lens within 60 cm of sea level, and 2) the Anchialine Cave Assemblage living in the saline groundwater. Helenina anderseni, Discorinopsis aguayoi, and other marsh foraminifera can persist in the brackish meteoric lens, which transitions into a more diverse assemblage dominated by Bolivina striatula and Rosalina globularis below the halocline. The boundary between the anchialine (terrestrially dominated) and submarine cave (marine-dominated) environments is demarcated by gross foraminiferal and sedimentary changes (δ13Corg from −24‰ to −18‰, C:N from 11.2 to 8.3) that correspond to the maximum point where terrestrial influences routinely impact the cave benthos. Three assemblages of foraminifera inhabit the submarine cave environment: 1) the Entrance Assemblage in the first ~60 m of the submarine cave, dominated by Quinqueloculina; 2) the Circulated Submarine Cave Assemblage dominated by Spirillina vivipara and Triloculina oblonga, and 3) the Isolated Submarine Cave Assemblage dominated by Spirophthalmidium emaciatum. Planktic tintinnids suggest that tidally forced saline groundwater circulation is transporting more nutrients and particulate organic matter to the Circulated Submarine Cave Assemblage than the Isolated Submarine Cave Assemblage. These results indicate that coastal caves are partitioned into specific environments that can be further subdivided into habitats by groundwater masses, sediment fluxes (terrestrial versus marine), and groundwater circulation. This implies that that cave foraminifera can be useful paleohydrogeologic, paleoclimatic, and Quaternary sea-level proxies.