The article deals with the development of the mobile environmental monitoring system and the peculiarities of algorithm design using aerospace technologies. The authors have proposed the methodology for designing the ecological risk zones based on the ranking methods of ecological indexes with the multi-criteria environmental safety assessment of the ecosystem, based on the use of multispectral characteristics of the space image. The methodology for defining the ecological risk zones has been proposed, which is based on the ranking methods of ecological indexes using one of cluster analysis tools – the hierarchy analysis method. The proposed approach can be efficiently used to define the ecological risk zones, choose the ways of the ecological rehabilitation of damaged areas and construct the prospective ecologically clean and safe regions. The proposed methodology for synthesizing the ecological risk zone based on the multi-criteria selection has been studied on the example of defining the most dangerous zone after the environmental monitoring. The article proposes the research and methodological basis, which helps to define the ecological risk zones directly based on the set of ecological indexes and turning the criteria into the complex (scalar) index. The prospective to develop the proposed approach is to improve it so that it could take into account the instability and stochasticity of the ecosystems under consideration. The authors have proposed to assess the risk of threats to the ecological, natural and technogenic safety of the regions. The intensity of emergencies has been statistically estimated in the article. The probabilities of the threatening environmental situation and safety functions of the considered ecological risk zone have been defined. The approach, considered in this article, will help to improve the efficiency of managerial decisions on ensuring the environmental safety, to find the best compromise between the contradictory quality indexes of system operation, to select and substantiate the priority directions for the development of complex ecosystems. The article provides the necessary research and practical recommendations for applying the mobile system of aerospace environmental monitoring.