The study of buried landforms during engineering–geological surveys is considered. The necessity of tracing and comprehensively studying Quaternary channels, troughs, and other cuttings, which may inherit lineament zones, is shown by the example of the Balakovo NPP site, which belongs to especially hazardous and complicated engineering objects. These zones show high water permeability and weak physicomechanical properties of soils. The structural geomorphological, geological, and hydrogeological conditions at the Balakovo NPP site were investigated. Most of the data were obtained from borehole cores. Ten lineament zones, following paleocuttings in the buried relief, were identified. On the Earth’s surface, they are marked by small depressions, which are interpreted as lineaments on satellite images. The long-term geodetic observations over deformations of ground bases of NPP buildings revealed uneven deformations and tilts at the compartment units 1–4 of the reactor. The tilting direction more or less fits the location of paleocuttings filled with deposits of different composition and structure. The groundwater and confined aquifers are redistributed there, and subsurface erosion may also occur. Thus, to predict the behavior of ground bases of buildings and engineering structures, it is necessary to consider buried landforms related to the specific structure of the Quaternary alluvial soils and local variability of their physical and mechanical properties.