The tectonic structure of an aquifer can influence the dynamics of groundwater flow with effects on the aquifer's vulnerability. In an area located in Salento Peninsula, characterized hydrogeologically by a multi - aquifer system, superimposed on the deep aquifer, that prove to be heavily salsified even in the internal areas, a qualitative deterioration of the shallow aquifer used for irrigation starts taking place. A joined analysis of the dynamics of groundwater circulation in relation to the morphotectonic asset of the area, reconstructed on a detailed geologic model implemented on a density dependent flow model, has pointed out the influence of the tectonics on groundwater flow behaviour and on the exchange phenomena between the two aquifers, explaining therefore the increment in groundwater salt concentration.