Sustainable use of marine water areas is one of the priorities of preserving biodiversity and the environment as a whole. The problem of a clear plan of rehabilitation measures, which would be based on complex and balanced solutions arises for their effective restoration and further functioning. These decisions should take both environmental and economic aspects into account. Estuaries, unlike marine water areas, are more sensitive to anthropogenic and climatic changes. They are characterized by shallow water level, functioning in the conditions of limited water exchange, dependence on river flow and greater anthropogenic load compared to marine water areas. These features are the cause of more intensive changes in the structure of biocenoses, rise in emergency situations, loss of productivity and sustainability of ecosystems as a whole. Thus, there is a need to introduce environmental management for these reservoirs, which should be based on a multi-component decision support system. This system will make it possible to develop clear plans for the restoration of marine ecosystems and prevent negative changes and degradation in them. The proposed scheme for developing plans for the restoration of the ecosystems of estuaries is represented by three blocks. The first “Block of data collection” involves the implementation of 3 stages: assessment of the current state of the reservoir; definition of problems and their ranking; assessment of ecosystem services. The second block “Search for a solution” is based on 4 components: Component 1. Database management system; Component 2. Geoinformational system; Component 3. Mathematical and predictive models; Component 4. Informational and management system for choosing strategic and operational decisions. The third block “Implementation of measures” involves the implementation of 4 stages: environmental assessment of decisions and projects, implementation of environmental measures, evaluation of effectiveness, search for new solutions and their improvement. The proposed scheme will enable a comprehensive approach to the restoration of estuarine ecosystems and ensure their sustainable use.