Abstract: This study refines the hydrogeological conceptual model of an area with three interconnected aquifers, namely the Crystalline Aquifer System (CAS – igneous and metamorphic rocks), which is in contact with the Tubarão Aquifer System (TAS – sedimentary rocks) and the Diabase Aquifer System (DAS – diabase rocks). The detailed investigation involved geophysical logging and hydraulic and hydrodynamic characterization with straddle packers in a local tubular well, in which groundwater presents high uranium concentrations. Hydrogeochemical and isotope (δ2H, δ18O, 3H, δ13C, 14C) analysis in this well and in other three neighboring wells, with lower U concentrations, showed that ancient and modern waters (3H from <0.8 to 1.12 TU, 14C from 69.43 to 78.72 pMC) mix within the aquifer. During groundwater pumping, vertical fractures in the diabase aquifer possibly induce water mixing and recharge of the deeper levels of the aquifers from shallow layers. The high [U] are related to ancient waters from a confined aquifer hosted in CAS that reaches the wells through hydraulically active fractures located deeper than 159 m depth. Groundwater apparent ages do not increase systematically with depth, revealing a complex circulation model for CAS. The results obtained from the other wells, which are all located on drainage lineaments, reveal that one extracts modern water from DAS and TAS, another one extracts modern and ancient water from DAS and CAS, and the third extracts only ancient water from CAS, confirming the complexity of the local hydrogeology. Regarding regional groundwater management, the study revealed the need to characterize the sources of groundwater in each well, in order to protect modern waters from anthropogenic contamination and to protect ancient groundwater from overexploitation, as CAS hosts groundwaters recharged thousands of years ago or more.