Simulation study by means of coastal ecosystem model is conducted to examine the various effects of Phase-II Mega-Float model on marine environment in Tokyo Bay. As several results of field measurement around Phase-II Mega-Float model, some local impacts on marine chemical-biological environment were found; the amounts of chlorophyll-a and dissolved oxygen decrease, and the nutrient concentration increases under the floating structure. These phenomena are thought to be caused by the sessile organisms adhering to the floating structure, and are reproduced adequately by improving formulation of the biological processes related to the sessile organisms. Finally, the impacts of Phase- II Mega-Float model on the surrounding marine environment are discussed.