The successful application of water quality models is dependent on the reliability of the input data. In water quality modeling efforts, less attention has been made to the quantity of water compared to the water quality-related parameters. To estimate the pollution loadings for a water system, concentrations of pollutants and flow rates of tributaries entering the system must be known. In Korea, the flow rate data are not always available for tributaries. Therefore, the estimation of tributary flows has been one of the major obstacles in water quality modeling analysis. In this study, several methods are tested to indirectly estimate the flow rate of major tributaries of the Han River, where the routine measurements are not reported. Alternative methods are studied using 1) the difference of flow rates between two known locations of major stream and allocating the difference proportional to the basin area of each tributary, 2) empirical formula such as Manning’s equation or rational methods, and 3) known relationship between basin areas and discharges obtained from major dams operation records in the river system. The alternative 3) is proved to be simple and reliable enough for the purpose of the water quality modeling. An excellent linear relationship is obtained between runoff and catchment area in log-log scale. The results slow excellent agreements with observed data