Most of the Mediterranean coastal porous aquifers are intensively exploited. Because of climatic and anthropogenic effects, understanding the physical and geological controls on groundwater distribution and flow dynamics in such aquifers is crucial. This study presents the results of a structural investigation of a system located along the coastline of the Gulf of Lions (NW Mediterranean). A key aspect of this study relies on an onshore-offshore integrated approach combining outcrops, seismic profiles, and borehole data analysis. This multidisciplinary approach provides constraints on pore-fluid salinity distribution and stratigraphic organization, which are crucial in assessing the modes of groundwater/seawater exchanges. Onshore, Lower Pliocene deposits dip gently seaward. They are unconformably overlain by Holocene clays in the lagoons. Offshore the Pliocene deposits either outcrop at the seabed or are buried below nonconsolidated sands infilling paleo-valleys. Beneath the lido, the groundwater salinity distribution consists of salty pore water, overlying fresher pore water. Active circulation of groundwater masses is inferred from the geophysical results. In particular, offshore outcrops and paleo-valleys may play an important role in salt water intrusion.