The article reviews the issues concerned with correctness of the engineering-geological and hydrogeological assessment of the Upper Kotlin clays, which serve as the foundation or host medium for facilities of various applications. It is claimed that the Upper Kotlin clays should be regarded as a fissured-block medium and, consequently, their assessment as an absolutely impermeablestratum should be totally excluded. Presence of a high-pressure Vendian aquifer in the lower part of the geological profile of the Vendian sediments causes inflow of these saline waters through the fissured clay strata, which promotes upheaval of tunnels as well as corrosion of their lining. The nature of the corrosion processes is defined not only by the chemical composition and physical and chemical features of these waters, but also by the biochemical factor, i.e. the availability of a rich microbial community. For the first time ever, the effect of saline water inflow into the Vendian complex on negative transformation of the clay blocks was studied. Experimental results revealed a decrease in the clay shear resistance caused by transformation of the structural bonds and microbial activity with the clay’s physical state being unchanged. Typification of the Upper Kotlin clay section has been performed for the region of Saint Petersburg in terms of the complexity of surface and underground building conditions. Fissuring of the bedclays, the possibility of confined groundwater inflow through the fissured strata and the consequent reduction of the block strength as well as the active corrosion of underground load-bearing structures must be taken into account in designing unique and typical surface and underground facilities and have to be incorporated into the normative documents.