The sustainable use of natural renewable resources represents one of the main tasks of the twenty-first century. The renewable geothermal resources can be profitably employed for energy production, heating and in several industrial processes allowing the reduction of the greenhouse gases and the human footprint. The knowledge of the main features that favor the development and the renewability of a geothermal system is the subject of detailed studies. In this context, numerical models reproducing the 3D geological setting of a geothermal system represent a tool to evaluate the involved geological and physical processes. The results can be used to perform site specific plans for a sustainable exploitation of the resource preserving it for the future generations. This procedure was adopted for the first time in the case study of the Euganean Geothermal System (EuGS; Veneto Region, NE Italy). Approximately 15 million cubic meters per year of thermal waters with a temperature ranging from 63 to 87 °C are exploited by approximately 200 wells. The Euganean thermal water is of meteoric origin and infiltrates an elevation of about 1500 m a.s.l., as suggested by its stable isotope composition. The recharge area is located on the Veneto Pre-Alps, approximately 100 km to the north of the exploitation area. The high-angle NE-dipping faults that characterize the central part of the Veneto Region allow the groundwater flow from the recharge area to the exploitation area. In the latter, a pattern of local fractures deforming the bedrock favor the rising of the thermal fluids toward the surface. The waters are mainly used for recreational purposes, producing an income of 300 million euros per year. To maintain this natural resource a detailed numerical model based on coupled simulation of fluid flow and heat transport was performed. Being the existence of this geothermal system related to a particular geological and structural setting, a 3D geological reconstruction was achieved by the use of MOVE software. The geological model was implemented into the numerical model through an unstructured mesh with the aim of maintaining a high geological detail. The results achieved by the numerical model allowed both to explain the geological processes that characterize the EuGS and to evaluated its renewability. The unravelling of these processes and of their interplay will allow to perform a management plan for the sustainable exploitation of the Euganean thermal water.