Background . The construction of a nuclear power plant inevitably requires excavation of a deep pit. This task may be impeded by high groundwater levels. The groundwater inflow into the pit can be limited by erecting a cut-off wall. As a rule, the cut-off wall is deepened to the aquitard elevation; however, the presence of hydrogeological windows therein may reduce the efficiency of such a solution. Aim. To determine the nature of clay layer deformation along the regional dislocation area of the Paks II NPP construction site. Materials and methods . A comprehensive geological and hydrogeological study was carried out to identify the continuity of the clay layer. This included an analysis of core samples from more than 1000 engineering and geological boreholes, surface and borehole geophysical surveys, a multi-level borehole network for groundwater level monitoring, as well as numerical hydrogeological modelling. Results . It was found that extensive borehole data does not always guarantee the sufficiency of information for mapping the hydrogeological settings. The continuity of the clay layer with a vertical displacement amplitude of 100 meters was established through a probabilistic analysis using a numerical model and a set of hydrogeological surveys aimed at confirming or refuting the modeling results. Conclusion . Assessment of hydrogeological conditions when implementing high-risk projects, such as nuclear power plants, underground excavations, and open-pit quarries, determines their safety and economic feasibility. In the absence or inconsistency of geological structure knowledge, hydrogeological surveys can serve as an independent source of missing information.