SWAT model was applied to estimate daily stream flow for Yongdam and Bocheong watersheds in Korea. The model was calibrated and validated for the two watersheds and a new routine was added to analyze runoff process in paddy fields. The model efficiencies for two watersheds were 0.77 and 0.65 for the calibration period, and 0.76 and 0.50 for the validation period, respectively. It showed that water balance method simulated the runoff from paddy fields more precisely than CN method in SWAT. As results, the SWAT model is applicable to Korean watersheds, and more accurate estimation is possible using daily water balance method in paddy fields.