Non-point source pollutants in down stream of Nakdong river were simulated by SWAT. GIS was utilized to make input data of SWAT such as landuse pattern and soil. Meteorological data of 2007 and 2009 were applied for the calibration and validation of runoff in SWAT. It was difficult to calibrate and validate the runoff and nutrient results since a study area was influenced by the tidal effects. Jindong site was selected to escape from the bias of runoff simulation in the coastal area. $R^2$ values of calibration and validation were 0.8 and 0.79. However, $R^2$ values of water qualities were very low level in comparison to runoff. These resulted from the concentration scale of water qualities such as BOD, T-N and T-P. Additionally, tidal influence could effected on the measurements of nutrients. The simulated annual averages and patterns of BOD, T-N and T-P in SWAT were similar to the measurement data. 80 ~ 96 % of nonpoint source pollutants at Nakbon M site were released from April to August of 2009. The ratio of T-N and T-P from nonpoint source were above 50 % during the rainy season.