This work sets out a methodology of integrated geological, hydrogeological and geophysical surveys for the characterization of contaminated sites. The flow model of the shallow aquifer in the Brindisi area (recognized to be at significant environmental risk by the Italian government) and the impact of an antrophic structure on the groundwater flow have been evaluated. The stratigraphic and hydrogeological targets used for the calibration phase of the flow model provide a means of assessing calibration quality. The good calibration of the model point out the key role of a detailed knowledge of the physical-stratigraphycal attributes of the area to be studied and field data collection. Geoelectrical tomography focus the attention on an area resulted of particular interest by the flow model obtained. This method permit to reconstruct in detail the lateral and vertical lithological variations in the geological formations improving the spatial resolution of the data and consequently the scale of observation. Besides, anomaly resistivity values have been correlated with pollution. Chemical analysis have confirmed this correlation.