For Kangjeong stream and Akgeun stream in the central part of the southern Jeju Island, on-site discharge estimation was carried out for approximately 10 months (July 2011-April 2012) twice a month on a regular basis by using ADCP (acoustic doppler current profiler) and long term rate of discharge was calculated by using SWAT (soil and water assessment tool) model. The discharge was $0.28-1.30m^3/sec$ for Kangjeong stream and $0.10-1.54m^3/sec$ for Akgeun stream. It showed the maximum in the summer and the minimum in the winter. As a result of parameter sensitivity analysis of SWAT model, CN (NRCS runoff curve number for moisture condition II), SOL_AWC (available water capacity of the soil layer), and ESCO (soil evaporation compensation factor) showed sensitive responses. By using the result, the model was corrected and the rate of discharge was calculated. As a result, the annual discharge rate was 27.12-31.86(%) at the Akgeun basin and 23.55-28.43(%) at the Kangjeong basin.