The hydro-geological conditions of Tomsk are determined by both natural factors and the impact of the urban infrastructure. Important impact on subsurface water flows involves the complex hydraulic relationship of several geological layers and the ancient and modern relief. Increasing groundwater abstraction has generally led to lowered piezometric heads in the deeper aquifer horizons, while in the uppermost horizons, rises in the water table and formation of new perched water tables are experienced due to leaking pipes and impedance of groundwater flow by deep foundations. In this paper special attention is paid to the Quaternary aquifer complex. Barrage effects of pile foundations and the intensive development of perched water distributed on flat surfaces of the watersheds and high terraces, complicated conditions for the construction and operation of facilities, leading in some cases to emergency situations.