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The present paper is aimed at studying hydrophilic and hydrophobic interactions via the modeling behavior of carbonate-clayey soil in a laboratory experiment. The typical aspects of human impact on the biogeochemical processes of natural soils such as decompression, disintegration, hydration and introducing easily oxidized organic matter were simulated. The experimental settings were adjusted regarding common field conditions for the clay near-surface layers in the temperate zone. The model system consisted of a carbonate-clayey soil, filtering water, and a psychrophilic microbial community desorbed from cave calcite formations (speleothems). The carbonate-clayey soil was collected from eluvium on red clay bedrock deposits of the Permian system along the right bank of the Volga River in the Republic of Tatarstan. The microbial community was stimulated with a modified R2A growth medium and inoculated into the clay using ceramic carrier discs. In order to explain the results of the experiment auxiliary materials presented simplified systems of the carbonate clay components were used. Soil properties such as the size distribution of mechanically strong particles and microaggregates, mineral composition, organic matter content, water wettability, and the chemical composition of filtered water were determined. The experiment being carried out during six months showed the appearance of new hydrophobic contacts between soil particles, crystalline cement deposition and the high sensitivity of these processes to microbial activity. The results of the study may help in understanding the processes that occur when foundations for constructions or underground facilities contact microbially produced substances, as well as predicting soil weathering.