The typical situation of technogenic influence on biogeochemical processes of previously unaffected soils of the terrigenous carbonate complex was simulated experimentally. The dynamics of some physical, chemical and physico-chemical properties of the model system consisting of: a carbonate clay soil, filtering water, and a psychrophilic heterotrophic microbial community washed away from calcite speleothems, was investigated. The carbonate clay soil was sampled from eluvium on red clay bedrock deposits of the Permian system. The rock to extract the psychrophilic microbial community was selected from the aphotic zone of the Yuryevskaya cave, Republic of Tatarstan. The microbial community was stimulated by the modified R2A nutrient medium. We used standard methods to determine the soil and filtrate physical and chemical properties, as well as the captive bubble method in the author's modification for wetting contact angle of soils. The experiment showed that the model technogenic impact on the carbonate clay soils modified their properties. The microbial activity during 6 months caused a redistribution of microaggregates in size, increased the fraction of crystalline contacts between soil particles, immobilized some inorganic ions, and increased soil heterogeneity and hydrophobicity. The results of the study can be considered when designing the foundations for constructions contacted with organic substances, weathering soil behavior predicting, as well as when planning caves’ restoration and preservation.