In the planning of the improvement works of fishing port, it is important to pay a deep consideration to the surrounding environment in order to keep the fishing ground sustainable as much as possible, since the fishery depends on the natural resources. In this study, ecosystem in the shallow sea around Koshigoe fishing port, where is rich in seaweed, was investigated. In order to reduce the impact of the extension of the breakwater, a method to select optimum location was given, based on the distribution of the seabottom less covered with seaweed.