Stable hydrogen and oxygen isotope signatures of waters within Church and Inkwell blue holes are measured on San Salvador Island (Bahamas) to identify the origin of their fresh and saline waters. Stable isotope data, paired with a suite of physicochemical water parameters measured throughout the blue holes, as a function of both time and depth, provide a detailed understanding of the tidally influenced groundwater interactions on the island. Blue holes are prominent karst features in carbonate environments which serve as windows into subterranean hydrologic processes. Carbonate island hydrology is often complicated by complex interactions between the marine and meteoric water systems, as tidal pumping and water mixing result in diagenetic alteration of the bedrock, that in turn influence dissolution rates and preferential flow paths. Although the blue holes on the island are physically influenced by tidal forcing, the stable isotope data indicate that both their fresh and saline waters are of a meteoric origin rather than seawater, where the meteoric water is likely becoming saline through enrichment by aerosol-derived sea salts. Additionally, the physical profiles of each blue hole indicate differences in mixing processes driven by wind and tidal forcing, where stronger mixing can result in a disruption of the freshwater lens. The implications of this study are important for assessing mixing corrosion processes and dissolution effects, but more research and longer data sets are needed to show whether these results are applicable to other coastal carbonate environments.