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Carbonate lithologies host considerable quantities of the Earth's freshwater resources and partially supply a quarter of the global population with drinkable water. In addition, carbonates constitute substantial amounts of the global coastlines, yet it is not known if and how they can sustain freshened groundwater offshore. Here, we use controlled-source electromagnetic, seismic reflection, and core sample data to derive a lithological model for the eastern margin of the Maltese Islands and identify four distinct resistivity anomalies within the Upper Coralline and Globigerina Limestone formations. The anomalies hosted in the former are likely associated with low porosities, whereas the anomaly within the latter is indicative of pore fluid freshening. Hydrogeological modeling suggests that freshened pore fluids, emplaced during sea-level lowstands and preserved in low permeability units, are potentially still found within carbonate shelves. However, resource potential is low due to its relict nature and low permeability host environment.