The Mekong River is an attractive river basin because of many natural environmental and development projects. Also, the river basin is located in six different countries and the basin countries are composed of different situations of economic, culture, history, policies of planning of the river basin, etc. There is considerable world interest in the large Mekong river. The authors propose a new approach to planning river basin management of this river basin to be sustainable for the future. The Hydro GIS is the unique method of flood simulation and appropriate methods to clarify flood status on low relief floodplains such as the Mekong delta.