A decision support system DSS-WQMRA (Decision Support System-Water Quality Management in Rural Area) was developed to help regional planners for the water quality management in a rural basin. The integrated model DSS-WQMRA, written in JAVA, includes four subsystems such as a GIS, a database, water quality simulation models and a decision model. In the system, the GIS deals with landuse and the location of pollutant sources. The database manages each data and supplies input data for various water quality simulation models. the water quality simulation model is composed of the GWLF( Generalized Watershed Loading Function), PCLM(Pollutant Loading Calculation Module) and the WASP5 model. The decision model based on mixed integer programming is designed to determine optimal costs and thus allow the selection of managemental practices to meet the water quality criteria. The methodology was tested with an example application in the Bokha River Basin, Kyunggi Province in Korea. It was proved that the integrated model DSS-WQMRA could be very useful for water quality management including the non-point source pollution in rural areas.