The software environment for the formation of a comprehensive assessment of the ecosystem state is considered, which provides obtaining information of various types, organizing the database and combining heterogeneous data on a single metrological basis, allows the expert-ecologist to form the functional of the ecosystem state assessment taking into account the specifics of the area, the type of production or several industries, the scale of impact on the environment. The modeling system provides pro-forecasting of situation development, the possibility of designing territories, and environmental management.