Columnar buildups found in a tidal channel off Lee Stocking Island, Exuma Cays, Bahamas, have been interpreted as modern giant stromatolites growing in a subtidal normal marine environment. However, these organically-formed columns reveal three discernible internal structures: (1) prokaryotic stromatolites comprised of alternating layers of coarse-grained ooids and peloids, and fine micrite that formed exclusively by microbial activity; (2) eukaryotic stromatolites comprised of microbially-induced micritic layers alternating with detrital layers accumulated, bound, and cemented by eukaryotic algae; and (3) thrombolites displaying irregular, clotted fabrics and formed by microbes, algae, and metazoans. Phanerozoic thrombolites, in contrast, have been interpreted as unlaminated stromatolites constructed by cyanobacteria. Eukaryotic organisms overgrow all of the columns at present. Thus, the contemporaneous formation of prokaryotic stromatolites, eukaryotic stromatolites, and thrombolites under identical conditions within the present environment appears unlikely. We suggest that the prokaryotic stromatolites represent forms that began to develop in an intertidal setting with the Holocene flooding of the Great Bahama Bank. The thrombolites, however, began to form under the present, normal-marine subtidal conditions. The eukaryotic stromatolites represent intermediate forms between prokaryotic stromatolites and thrombolites. There is evidence for a gradual change from stromatolite to thrombolite reefs associated with rising sea-level. With the deepening, there would have been a decrease in salinity, an increase in energy, and possibly an increase in nutrient supply; all factors that favor thrombolite growth. We propose that the co-existing stromatolites and thrombolites found off Lee Stocking Island did not grow contemporaneously, but reflect a response to changing environmental controls with changing sea-level.