We need to analyze the ecological characteristics in the basin of agricultural reservoir that include urbanized area, agricultural area and fringe area, etc. The purpose of this study is not only that presenting the methods of basin ecosystem management but also suggesting ecosystem management plan proposals for the water quality based on analysis of ecological characteristics. As the results of analysis, the urbanized area(the ratio of area(ROA): 14.0%) is most likely to possibility of water pollution, then followed by paddy fields(ROA: 65.5%) where a wide spread up-basin(or up-stream), farmlands(ROA: 11.3%), farm buildings(ROA: 5.7%) and orchard(ROA: 3.9%). According to those, we investigated the impact degree of water pollutants. Thus, we were able to classify 5 types through considering the biotope assessment and the hydrosphere basin assessment, i.e. the level of priority control for source pollution. As a result, the source pollution intensive management area(11.3%) where are adjacent waterfront has caused water pollution, however, most importantly, it is necessary to control in source pollution management area(0.6%) that are away from waterfront. In conclusion, according to the these results, the plan of basin ecosystem management for the water quality should be included the plan of ecosystem conservation and restoration such as improving inhabitants function, controling environmentally sound basin management, promoting biodiversity.