In order to strengthen flood risk management in a river basin, to upgrade the capability of flood control, and to reduce the losses of lives and properties in urban areas, a numerical simulation model was proposed in this study on the basis of 2D shallow water equations. A satisfactory result has been obtained by applying it into the Fuji River basin in the central Japan. Results indicate that the numerical simulation model proposed can be adopted not only in risk management of a river basin, but also in the study of real time operations of rescue jobs and evacuation routes in a municipal region suffering from a serious flooding event.