In this study, we developed a program to estimate discharge efficiently considering major hydraulic characteristic including water level, river bed, water slope and roughness coefficient in a natural river. Stream discharge was measured at Gongju gauge station located in the down stream of the Daechung Dam during normal and dry seasons from 2003 to 2004. The developed model was compared with the results from the existing rating curve at T/M gage stations, and was used for runoff analyses. Evaluating the developed river discharge estimation program, it was applied during 1983-2004 that base flow separation method and RRFS (Rainfall Runoff Forecasting System) which is based on SSARR (Streamflow Synthesis And Resevoir Regulation). The result presents the stage-discharge curve creator range at the Gong-ju is overestimated by approximately $10-20\%$, especially at the low stage. It is attributed to the hydraulic characteristics at the study. The discharge simulated by the RRFS and base flow separation, which is calibrated using the measurement at the early spring and late fall season during relatively d]v season, shows the least errors. The coefficient of roughness at Gongju station varied with the high and low water level.