The water of rivers and lakes in Korea is the main sources for drinking, industrial and agricultural purposes. However, various pollutants washed-off from watershed area make worse and worse the water quality. Particularly, the changes of land uses in watershed area is the main pollutant sources in many cases in Korea, it is usually called to nonpoint pollution sources. In this reason, the Ministry of Environment are programing the total maximum daily load for four major large rivers in order to improve the water quality by controlling the watershed area. Therefore, this research was performed to estimate the total pollutant input from watershed areas to lakes of Ganwol and Boonam located in Chungnamdo. The AGNPS water quality model and monitoring were used to estimate the pollutant loading rates with unit pollutant concentration of each land use. The main landuse of the research area are forest, wet and dry paddy field and small urban area. The research shows that the pollutant sources in Ganwol and Boonam lakes are from the various landuses. In this manuscripts, the results will provide important informations for mitigating the pollutants to the lakes.