Soil Organic Matter (SOM) is a highly active component involved in aggregate formation, however the physical mechanism of its influence is not yet uniquely determined. While the role of SOM in forming a water-stable structure is logically evident and widely accepted, the structure formation itself and the mechanism of water stability still remain discussible. As the research target we have chosen a typical chernozem area, located in the Central Chernozem Reserve, under conditions of virgin grassland steppe and arable land, which has been a fallow land since 1947. Considerable changes have taken place on macro- and microaggregate levels, as well as in soil density and filtration: a fall-through filtration ability of steppe upper horizons has lowered from 1.3 to 0.3 mm/min, significant packing of upper horizon (0.601-0.752 g/cm3-steppe, 1.050-1.309 g/cm3 arable land) has occurred, aggregates have lost their water-stable property. In arable chernozems some evident modifications of SOM content have been registered. At similar absolute values of humic acid content, the mineralization of SOM in the arable horizon is accompanied by an increase in its humicity and the reduction of the Cdetritus : Cakt ratio, as compared with the steppe humus-accumulative horizon A1. Obviously while the humus humicity grows, a visible deterioration of soil structure takes place. This statement somewhat contradicts with generally established characteristics of humic acids, as essential builders in water-stable structure formation, and points out the role of fulvic acids. The hydrophobic interaction chromatography enables to identify hydrophilic, as well as hydrophobic components in a SOM composition. The chromatographic analysis of the steppe and arable land's SOM showed that long-term chernozem cultivation has resulted in the significant reduction of the absolute content of hydrophilic components of SOM in the arable horizon and the increase of such in the underlying ones. Furthermore it indicates less resistance of these humus components to chemical and microbiological destruction on one hand, and the mobility of hydrophilic SOM within a soil profile on the other hand. The content of hydrophobic SOM is noted to remain constant. The research results make it possible to build up a first approximation for the model of structure-functional organization of hydrophobic-hydrophilic SOM components in a chernozem soil aggregate. The humification of organic matter in situ within the mineral horizons of a soil profile results in the formation of a heterogenic SOM system. Its components differ in their hydrophobic-hydrophilic properties. Water-soluble (hydrophilic) humification products are carried out from decomposing plant residues. Being brought on a mineral surface, they participate in sorption and organic-mineral complexes. The mineral surface becomes hydrophobized, as a result of the mutual blocking of its own polar groups and the organic ones. The hydrophobic matter, incapable of water migration, stays in place of its origin, being isolated from mineral particles. Quasianaerobic conditions of humification promote an accumulation of hydrophobic components inside the aggregate. The non-polar molecular fragments determine its hydrophobic properties on one hand and the resistance to oxidative mineralization and microbiological utilization on the other hand. The presence of the non-polar SOM inside the aggregate causes distortions in water structure. It can be transmitted at great distances through the chains of hydrogen bonds and cause long-range hydrophobic interaction. Combined action of the SOM hydrophobizing the mineral surface and the SOM localized in the microzones of nonpolar molecules stochastically distributed throughout the aggregate determines water-stable properties of the aggregate. The non-polar parts in aqueous medium attract each other, as being drawn together they minimize unfavorable contact with water. The total effect inside the aggregate hydrophobic zones consists in the resistance to rapid water entrance and the reduction of aggregate swelling. While the SOM on mineral surfaces is being mineralized, it exposes mineral hydrophilic surfaces and thus the effectiveness of hydrophobic interactions drops whereas the aggregates are being dispersed by water. This theoretical model of structure-functional organization of soil aggregates explains the changes, occurring in their water stability under long-term cultivation.