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Karst subterranean estuaries (KSEs) are created from the two- and three-way mixing of saline groundwater, rain, and oceanic water in the subsurface on carbonate landscapes, and this hydrographic framework promotes unique physical processes, biogeochemical cycling, and biological communities. Here we provide evidence that the source and quantity of particulate organic matter (POM) that is delivered to the benthos strongly correlates to benthic habitat partitioning in the oxygenated marine sectors of KSEs. A dataset of benthic foraminifera at 128 different locations from several large flooded cave systems in Bermuda were compiled and evaluated against common environmental characteristics (e.g., tidal exposure, substrate particle size, bulk organic matter, C:N, total organic carbon, and δ13Corg). Benthic areas receiving more carbon isotopically depleted organic matter sources (mean δ13Corg values < −23.2‰, C:N ratios >11), most likely from the terrestrial surface and some marine plankton, were dominated by Trochammina inflata, Bolivina spp., and Helenina anderseni. In contrast, benthic areas receiving more carbon isotopically enriched organic matter sources (mean δ13Corg values > −21.6‰, C:N ratios