An electrical resistivity survey was carried out on Thata Island, one of the numerous circular islands in the Okavango Delta, to investigate the mechanism governing the interactions between surface water, vegetation and groundwater. Seven profiles of data were collected across the island and the modelling results indicate that the centre of the island has low resistivity values (less than 10 ohm-m), while outside the island resistivity values increase laterally. This lateral resistivity zoning responds to variations of shallow groundwater chemistry below the islands with a high concentration of solutes inside and the presence of fresh water outside the islands. Results of borehole to surface resistivity imaging in the island indicate a sinking plume of saline water to depths of 60 m. Groundwater salinities below the island range from 11.7 g/l from margin of the island to 122 g/l at the centre of the island. Beyond the depth of 60m, the groundwater salinity drops to about 0.33 g/l at the centre of the island. Results of the lateral and down-hole imaging as well as water salinity values show a migrating plume of high salinity groundwater from the surface of the island invading a relatively deeper low-density fresh groundwater environment. The unique combination of geochemical, isotopic and electrical resistivity data indicate that capillary evaporation may be the most important mechanism in creating high saline waters under the center of the island, however high transpiration rates along the edges of the island may be important in producing salts that could migrate toward the island’s center. The results of this study show how high salinity levels may form in near surface aquifers in natural inland delta environments in semi-arid areas.