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In the framework of the final design of a new hydroelectric plant close to the existing dam on the Adige River in the municipality of San Giovanni Lupatoto (VR, Italy), the design of deep excavations in loose sediments below groundwater level, and the connected risks of piping and excavation bottom heave required a detailed study of hydrogeological characterization, aimed to an accurate aquifer parameterization and so a confident design of excavation supports and dewatering systems. Particularly a three-dimensional analysis of the problem was necessary, because the hydrogeological system was complicated by many “artificial” boundary conditions (dam on the river, deep foundations of the existing and new engineering works) causing vertical not negligible flow paths. The conceptual model has been developed applying, in parallel, different prospecting tools: a preliminary Step Drawdown Test, a long duration Constant Rate Test, a multiple tracing test and the implementation of a three-dimensional numerical model of groundwater flow (MODFLOW-2005 code) and advective transport (MODPATH code). The modeling has allowed a good estimate of the aquifer parameters such as hydraulic conductivity and effective porosity through calibration of the pumping/tracing tests under transient conditions. Moreover, the simulation of post operam conditions and the comparison with ante operam, in terms of flow paths length and filtration velocity, showed that the construction of the new works foundations would have determined a sensitive reduction of groundwater velocities closed to the existing dam.