A contamination by petroleum hydrocarbons was detected in a sandy aquifer below a petrochemical plant in Southern Italy. The site is located near the coastline and bordered by canals which, together with pumping wells, control submarine groundwater discharge toward the sea and seawater intrusion (SWI) inland. In this study, a three-dimensional flow and transport model was developed using SEAWAT-4.0 to simulate the density-dependent groundwater flow system. Equivalent freshwater heads from 246 piezometers were employed to calibrate the flow simulation, while salinity in 193 piezometers was used to calibrate the conservative transport. A second dissolved species, total petroleum hydrocarbons (TPH), was included in the numerical model to simulate the plumes originating from light non-aqueous-phase liquid. A detailed field investigation was performed in order to determine the fate of dissolved hydrocarbons. Fifteen depth profiles obtained from multilevel samplers (MLS) were used to improve the conceptual model, originally built using a standard monitoring technique with integrated depth sampling (IDS) of salinity and TPH concentrations. The calibrated simulation emphasises that density-dependent flow has a great influence on the migration pattern of the hydrocarbons plume. This study confirms that calibration of density-dependent models in sites affected by SWI can be successfully reached only with MLS data, while standard IDS data can lead to misleading results. Thus, it is recommended to include MLS in the characterization protocols of contaminated sites affected by SWI, in order to properly manage environmental pollution problems of coastal zones. © 2012 Springer Science+Business Media B.V.