Fluid flow and solute transport phenomena in fractured and karstic aquifers remain an open issue that calls the attention of numerous researchers belonging to different disciplinary fields as far as the aspects linked both to shallow and to deep phenomena are concerned. The hydrogeologic knowledge of these phenomena proves to be of high importance especially if considered in relationship with water resource exploitation, with the problems linked to contamination and the ones linked to urban and industrial development of the territory. In the examined area, characterized by a dismissed contaminated site, the realization of the landfill has required the development of a 3D flow model supported by a detailed local scale geologic model in order to evaluate the effects on groundwater flow and subsequently on contaminant propagation. The results of the flow model prove to be coherent with the fractured and karstic nature of the site in that they show at higher depths the presence of a subterranean stream channel that would speed up pollutant propagation. The obtained results represent the fundamental basis to implement a transport model that will permit to achieve a more in depth knowledge of the subsoil transport phenomena, and therefore to optimize any anthropic intervention that can involve the site.