In contaminated sites, remediation measures mostly depend on previous high-resolution site characterization (HRSC) results. In the case of industrial sites, where there is a high pollution risk for groundwater, many hydrogeological models are often achieved using stratigraphy results of geological drilling after the monitoring network design. This approach is only sometimes possible when contaminant back diffusion from small low-permeability lenses and layers occurs within a high-permeability aquifer. This framework needs a significant resolution that can be obtained by coupling preliminary stratigraphic data with specific in situ activities. Results from these additional investigations may help to locate low-permeability layers and, consequently, to identify the most vulnerable areas towards which groundwater management must be deepened. The use of gamma rays in combination with the analysis of the pluviometric and hydrometric data and together with the time series of the concentrations of a given analyte can provide indispensable support for site characterization, the development of numerical groundwater contamination models and remediation procedures when back diffusion occurs. In this study, within an industrial site in the province of Benevento (Italy), based on stratigraphy, a 3D hydrogeological model has been set up and coupled with results of natural gamma radioactivity logs to detect the release of Chromium VI from low-permeability lenses.