Carbonate margins form a significant portion of the world's coastlines, contain substantial freshwater resources, and play a vital role in global hydrogeological processes. These regions are promising reservoirs for offshore freshened groundwater (OFG), a potential resource for coastal and island populations. Mapping OFG within continental margins using marine controlled-source electromagnetic (CSEM) data relies on electrical resistivity as a proxy, requiring sophisticated inversion techniques. Given the ambiguity in deriving discrete resistivity distributions from CSEM data, understanding uncertainty is essential for reliable OFG inference. The conventionally used two-dimensional deterministic inversion provides a best-fit solution but does not assess resistivity uncertainties, limiting OFG characterization. To address this, we apply trans-dimensional Bayesian inversion on marine CSEM data from a semi-arid carbonate setting off eastern Gozo (Maltese Islands, Mediterranean Sea). Here, we integrate deterministic and trans-dimensional inversion results with seismic reflection data to identify two distinct, continuous resistivity anomalies within the Lower Coralline Limestone formation. The first, shallower resistive body starts similar to 4 km from the coast, appearing across all the CSEM profiles at 210-250 m below sea-level, with resistivity increasing landward. This anomaly may suggest an OFG body. The second, deeper anomaly starts at 350-400 m below sea-level and extends deeper. Whether it represents a second OFG unit or geological changes remains uncertain. Our findings offer new insights into resistivity distributions within carbonate margins, highlighting their OFG potential and the value of trans-dimensional sampling. This study augments CSEM research, underlining the need to extend coastal hydrogeological studies offshore for improved environmental conservation and resource management.