The water quality in Osaka Bay has been chronically bad because of the typical enclosed sea of the high pollution load. Environmental simulation model is necessary to construct an environmental management system for not only sea but also land area. In this research, we develop an ecosystem model for the enclosed sea with reference to the results of field investigations at Yura harbor area in Osaka bay. The results of the numerical simulation clarify the changes in water quality in Yura area, and also show some problems of environmental simulation for coastal area.