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A numerical model that treats density-dependent variably saturated flow and miscible salt transport is used to investigate the occurrence of seawater intrusion in the ‘Korba’ aquifer of the eastern coast of Cap-Bon in northern Tunisia. We examine the interplay between pumping regimes and recharge scenarios and its effect on the saline water distribution. More localized simulations are used to examine, in vertical cross sections, the effects of well location and soil type and the role of the vadose zone in possible remediation actions. The exploratory simulations suggest interesting interactions between the unsaturated zone and the saltwater–freshwater interface with possible implications for groundwater exploitation from shallow unconfined coastal aquifers, involving in one case feedback between seawater intrusion and the high pressure head gradients around the pumping-induced drawdown cone and in another case threshold-like interface displacement for tight soils such as clays. The data processing steps undertaken in this GIS and modeling study are described in some detail, and a critical assessment is given of the data availability and of the requirements for successful monitoring and modeling of seawater intrusion risks in heavily exploited coastal aquifers such as those found in the semi-arid regions of the Mediterranean basin. It is shown how, with the aid of GIS, reasonably reliable information can be assembled from maps, surveys, and other sources of geospatial and hydrogeological data, an approach that is necessary in the many regions of the world with acute water resource problems but with limited means for undertaking systematic data acquisition and environmental monitoring actions. Nonetheless the need for more concerted monitoring of relevant parameters and processes and of closer coordination between monitoring and modeling is stressed. An idea of the extent of over-exploitation of the Korba aquifer is obtained by examining the pumping and rainfall/infiltration data, and the simulation results support groundwater pumping as the mechanism for and seawater intrusion as the origin of the salt contamination observed in the soils and subsurface waters of the Korba plain.