In the paper construction specificity of St. Isaak Cathedral’s underground space and engineering geological profile features are considered. The comparative assessment of condition and properties modification of water-saturated quarternary sandy and clay soils during 55 years are taken up (1954-2009). The dynamic of groundwater contamination due to leakage sewers and its aggressiveness are estimated. The researches of microbes activity in soils which are characterized by quasiheavy values are completed. The structural of complex monitoring to secure of St. Isaak Cathedral long-term stability are proposed.