The time domain electromagnetic method (TDEM) is applied to monitor, to delineate and to map the saltwater intrusion zones in the Mediterranean Plio-Quaternary aquifer. Forty-two TDEM soundings were carried out in the coastal plain of Nabeul–Hammamet region (NE Tunisia). TDEM resistivity data were correlated with the existing borehole logging data to assign them to a particular lithology and to provide information about the position of the freshwater–seawater transition zone. The geoelectric sections showing the vertical configuration of seawater intrusion, with the brackish-salty-saturated zones, have a resistivity ranging from ~0.1 to 5 Ω⋅m and are detected at a depth lower than 1.5 m. The salinized zones are located at Nabeul (Sidi Moussa, Sidi El Mahrsi, Al Gasba and Mrazgua) and at Hammamet (Touristic zone of Hammamet north and south, Baraket Essahel) and reached a distance of 4 km from the coastline, indicating a severe state for the aquifer in these zones. These TDEM results are confirmed by the increase of chloride concentration content in the analysed water samples of monitoring wells. Moreover, in the northeastern part, the presence of a saltwater front located far from the coast and along the NW–SE major surface fault can be explained by two hypothesis: (i) this fault seems to provide a conduit for seawater to move readily towards the water wells and (ii) the clay and gypsum infiltration of marine Messinian deposits through the fault plane leads to low resistivities. Finally, it comes out from this study that TDEM survey has successfully depicted salinized zones of this coastal aquifer. Copyright © 2012 John Wiley & Sons, Ltd.