We have investigated the low terraces of the Ob and Tom rivers in the south of Tomsk Oblast, primarily the Ob–Tom interfluve area. This area is situated near Seversk and Tomsk suburbs, where 70% of the Tomsk Oblast population is concentrated. Rapid development of suburban areas and recreation activity, as well as pollutants, threaten the sustainable functioning of the terrace natural complex, where underground freshwater resources used by the citizens are replenished. This paper presents descriptions of ecological factors affecting low terrace soils in this interfluve area. We have studied the lithographic sequence of soil formation in the contact zone between the Aeolian dune and basin fields with sandy and sandy-loam soil-forming rocks and the flatbeds of the terraces with loam mantles undisturbed by Aeolian processes as soil-forming rocks. Protection of these soils should be established by legal instruments.