Current intensification and changes in agricultural land use practices increase environmental impact that can be reduced by bridging the gap between socio-economic demands and scientific justification of sustainable agricultural land use. This can be achieved by replacing the goal of maximum crop yields with the goal of minimal environmental impact. This paper presents results of integrated crop simulation system development for analysis of alternative planning strategies in agricultural land use, with focus on the crop rotation influence on environmental sustainability. The effective tools used in analysis include (1) long-term analysis of changes in agricultural land using a dynamic crop model with daily time step; (2) justification of arbitrary crop rotation scheme of different agro-technologies and sparing measures; and (3) analysis of modern farming management methods using model-oriented approach. The results of study also include estimation of two alternative practices of crop harvesting including remaining or removing whole crop residues from the agricultural field and their influence on basic parameters of soil fertility. In addition, we analyzed comparative efficiency of different agricultural measures neglecting the negative influence of possible climate changes in long-term consequences. Corresponding efficiency rating is the following: organic fertilizer, green manure legume sparing harvesting, winter catch crop, and rotation scheme.