The article presents the results of the analysis of the functioning of agroecosystems using optimization of the structure of agricultural ecosystems, conservation and reproduction of the natural resource base of the agricultural sector, exclusion and minimization of negative impacts on the environment. Agriculture should be considered as a huge, continuously operating mechanism for the protection and cultivation of living natural resources, and it should be approached from one point of view - environmental protection. Therefore, in conditions of agricultural production, the use of natural resources and, above all, land should be combined with environmental protection measures. Agroecology on the basis of an integrated system approach determines the ways of transition of agricultural systems to the basis of continuous development. The implementation of any agricultural projects requires environmental modeling and forecasting of negative changes that may occur. It is necessary to constantly monitor these changes, take measures to regulate the agricultural landscape, and maintain its reproduced properties at an optimal level. It has become necessary to expand the scope and increase the level of research aimed at ensuring the rational use of land and other natural resources on the principles of their regenerative capacity. That is, to form agroecosystems with an increasing particle of biologization of all technological processes.