A complex multiple aquifer system affected by a contaminated site and exposed to tidal effects was investigated to develop the hydrogeological conceptual model of the study case. Two water bodies were identified, from top to down: a surface aquifer unaffected by tidal events, and a semiconfined aquifer partly communicating with the brackish lagoon waters. By using the Cl(-)/SO4(2-) ratio and the DOC (Dissolved Organic Carbon) concentration, as well as by applying the kriking to the piezometric levels results, the groundwater flow directions and the hydraulic gradients within the investigated aquifers were also identified. Based on the overall results, a schematic of the conceptual model for the whole aquifer system was provided which allows to visualize the communication between the different water bodies.