A freshwater lake water quality management system(FLAQUM) was developed to help regional manager for the water quality of a rural basin. The integrated user interface system FLAQUM written in Visual Basic, includes three subsystems such as a database management system, basin pollutant loads simulation model using SWMM model and freshwater lake water quality simulation model using WASP5 model. Pollutant load simulation model was applied to simulate the discharge and pollutant loading from the watershed, and freshwater lake water quality model was applied to analyze the changes in water quality with respect to watershed pollutant loads, and this model could be used in planning to control watershed pollutant source for water quality management. Database management system was constructed fur all input and output data processing, and it can be used to analyze statistical characteristics using constructed data. Results are displayed both graph and text for convenience of user. The results of FLAQUM application to Boryeong freshwater lake showed that the lake was in eutrophic condition. The major contribution of pollution comes from tributary No.1 and No.4, which have a large number of livestock farms. Therefore, water quality management must be focused on appropriate management of the livestock farming in the two breanchs.