Central Chernozem is one of the largest agricultural regions in Russia. As a result of the long period of natural resources use the anthropogenic load on agricultural lands is increasing. The result of agricultural nature management is the increase of land degradation processes. Voronezh Region has a high agro-climatic potential, most of the territory is occupied by agricultural land, arable land prevails among them. Soil degradation is the most acute problem. There is a need to assess the impact of agricultural natural resources use on land resources of the region. Modular coefficients for assessment of geochemical impact of agriculture and animal husbandry on agricultural systems are proposed. The developed factor is a tool for identification of negative land use processes and environmental problems. The article deals with the issues of ecologically oriented, scientifically grounded strategy of agricultural nature management. Ecological approach to assessment of soil quality in the future will develop a strategy for balanced land use. The article has a scientific and practical character and is aimed at the development of methods of ecological assessment of soil quality. The proposed methodological approach identifies destructive processes in soils. For ecologically oriented strategy of development of regions it is important to define maximum allowable agricultural loads for preservation of sustainable environment.