The Brenner Base Tunnel (BBT) is being built to connect Italy with Austria. The southern access connects Ponte Gardena with Fortezza by two railway tunnels named Gardena and Scaleres. A 3D groundwater flow model, extended through an area of about 200 km2, has been built using MODFLOW code to evaluate the water inflow. The model thickness is 1200 m, divided into 8 layers varying from 100 m to 400 m. The model has been solved in transient conditions, allowing the water inflow both during 6 excavation stages reproducing the design excavation time schedule and during the subsequent equilibrium phase to be evaluated. Based on the geological and geotechnical model, the excavation methods have been defined; the results of the evaluation of water inflow and of the possible impact on the hydrogeological resources have been taken into account by defining risk mitigation measures to ensure hydraulic ante-operam conditions.