Purpose. The paper is aimed at describing the improved integrated model of the ecological-economic system "coast-bay" permitting to control the balance of rates of accumulation and destruction of the pollutants entering the sea with coastal runoff. Methods and Results. The model is based on the concept of mutual adaptation of the simulated processes’ deviations from their standard values under the influence of external forces. The average multi-year values of the simulated processes are used as a stationary state of the system. The scheme of the cause-effect relationships between the development of the biochemical processes in the marine ecosystem and the economic processes of consumption and reproduction of the marine biological and assimilation resources is proposed. The scheme contains the logical agents for managing the scenarios of these processes based on the criteria of the pollution and biodiversity levels of the marine environment. The system dynamic model was constructed using the method of adaptive balance of causes in which, in order to assess the influence coefficients, a new presentation of the normalized relations of the standard mean values is used. The current values of the simulated processes are used in the coefficient estimates. To test correspondence of the model scenarios to real processes, the computational experiments including the model of the ecological-economic system "coastal runoff-the Sevastopol Bay ecosystem" were performed. The observations-derived average multi-year values of phyto-, zoo-, bacterio-plankton, nitrates, ammonium, dissolved organic matter and detritus concentrations were used in the model. Conclusions. The results of the experiments confirmed possibility of managing the forecasted scenarios of the ecological and economic processes in accordance with the management concepts embedded in the model. The scenarios’ response to different variants of the external managing actions is shown, that makes such models a convenient tool for planning the nature-protection measures within the "coast-bay" systems.