The article proposes a developed expert information system for assessing environmental risks for complexly structured and uncertain source data. The result of using the program is the desubjectivization of the decision-making process in the presence of a large amount of heterogeneous information. It is supposed to use the system as a technical means of monitoring and assessing the harmful effects of military installations on the environment. The program should serve to increase the effectiveness of environmental protection measures at special facilities of the Ministry of Defense of the Russian Federation. The mathematical algorithm of the developed software application is based on the theory of fuzzy sets (Mamdani’s logical inference diagram). The solution involves finding the degree of truth and bringing to clarity the initially fuzzy input data by the centroid method and, as a result, a score assessment of the quality of environmental characteristics.