The inflow from Daejeo gate and the outflow from Noksan gate in Seonakdong river, which is a reservoir-like river with the characteristics of stagnant water, is very important for TMDLs (Total Maximum Daily Load) of Nakbon N unit watershed. However, there are very few measured data for calculating base flow. The operating data is much different from the actual measured data because the probable maximum flowrate is used for gate operation. In this study, the operating flowrate data of Daejeo and Noksan gates are compared with the monthly water quality data from Ministry of Environment monitoring station. The dynamic change of the flowrate and the water quality is also measured for the operation of Daejeo and Noksan gates. The flowrate of Seonakdong river is measured, which is affected by the gate operation, the water elevation difference of Nakdong river and Seonakdong river, and the tidal elevation. The results of this study can be used for establishing the water quality improvement measures by the optimal gate operation.