The construction of the nuclear power plant (NPP) requires conducting a large number of engineering and hydrogeological surveys, as well as assessment of the design decisions’ safety. A deep excavation pit at the Paks II NPP construction site requires execution of the cut-off wall due to extremely high groundwater saturation of the alluvial deposits. However, lithological anisotropy and the presence of dislocation zones did not allow identifying the appropriate depth for the cut-off wall construction. Unfortunately, engineering geological boreholes with a 20-meter distance between them and surface and borehole geophysical surveys could not identify the hydrogeological units. Thus, to conceptualize the hydrogeological settings, an analysis of the groundwater head distribution and the large-scale pumping tests were conducted. The interpretation of the geological data and the distinguishing of the hydrogeological units were carried out iteratively using the hydrogeological numerical model. The flow model could represent the hydraulic head distribution, the response of the lithologically heterogeneous layers to the water fluctuations in the Danube river, and the pumping tests carried out at the different depths. The results of the hydrogeological modeling revealed the aquitard to be continuous throughout the territory; however, its top’s depth changes from 30–35 to 90 m within the construction site of the Paks II NPP. This complex geometry of the aquitard is controlled by the plicated dislocation zone, which cuts the construction site in half and is revealed as the right wall of the graben.Correct hydrogeological stratification enabled us to ensure waterproof activities such as the cut-off wall construction using the hydrogeological model when excavating a deep pit for the Paks II NPP. This also minimizes the hydrodynamic impact on the closely located NPP Paks in operation.