With the aim of deepening our understanding of deep-seated fluids upwelling and mixing in large regional aquifers, we performed a hydrogeochemical study of twenty-two springs in the Contursi area (upper Sele river valley, southern Apennines) by means of the measurements of chemical-physical parameters, major ions, trace elements, and stable and radioactive isotopes. Besides, we realized two updated geo-structural cross-sections in order to reconstruct the groundwater flowpath in the study area. The hydrogeochemical composition, as well as the water temperature allow to identify-three main groups of groundwater: Cold and Low salinity Groundwater (CLGW), Intermediate Salinity Groundwater (ISGW), and Thermal Salinity Groundwater (TSGW). The CLGW group, mostly emerging at the boundary of carbonate aquifers, is characterized by alkaline earth-bicarbonate hydrofacies. Instead, ISGW and TSGW, situated in the inner zone of the valley, show gradually a hydrogeochemical evolution towards sodium-chloride type hydrofacies domain with the highest salinity value. Stable isotope (δ18O-δD) of CLGW reveal the local meteoric origin of groundwater, while isotopic signatures of ISGW and TSGW is associated with the deep fluids inflow. CLGW hydrogeochemistry is clearly related to dissolution of carbonate rocks. On the other hand, for ISGW and TSGW an additional contribution from evaporitic rocks is supported by saturation indices values (gypsum and anhydrite) and validated by isotopic signature of dissolved sulphate (δ34S-δ18O). The application of two models based on tritium data (i.e., the piston-flow and well-mixed reservoir) attributes longer and deeper groundwater flowpaths to TSGW. Through geothermometric calculations (e,g., K-Mg and SiO2-quartz), the equilibrium temperature of deep fluids reservoir is also extrapolated (i.e., 75–96 °C). The results of the adopted hydrogeochemical multi-component approach allowed us to propose an interpretative model of groundwater flowpath for the Contursi area, where deep-seated tectonic discontinuities play a significant role for the upwelling of saline deep thermal fluids in shallow aquifers.