Coastal diaster induced by waves and countermeasures were investigated in the viewpoint of reduction of overtopping rate with enviroment in fishing port. The reduction method of wave overtopping rate using ecosystem control structures was proposed and studied on the efficiency by hydraulic and numerical experiments. The estimation models on wave overtopping rate was proposed after comparing previous models with dimensional analysis and experimental results. Control function o fwave overtopping by use of ecosystem controlstructures was simulated and discussed with combining wave shoaling-dissipation-breaking deformation model around ecosystem control structures and newly proposed calculation model for wave overtopping rate. Feasiblilty of ecosystem control structures could be confirmed for reduction of wave overtopping and fisheries-based multipurpose development of coastal zone.