Flushing is a very complicated process in estuarine environments. In order to examine the effects of tidal amplitude, river discharge, and stratification on the spatially varying flushing time of the Sumjin River Estuary (SRE), 24 longitudinal salinity transects were obtained during spring and neap tides from August 2004 to April 2007. The widely accepted freshwater fraction method has been used to calculate the flushing time for multiple estuarine segments using a spatially varying freshwater fraction. The effects of tidal amplitude, river discharge, and stratification on estuarine flushing were identified reasonably well by the spatially varying time scale. The flushing time appears to be close to the semidiurnal (M2) tidal period during spring tide, but it is twice as long during a neap tide near the mouth. The flushing time increases in the central regions with a decrease in the tidal amplitudes and reduces in the inner-most regions owing to the strong influence of gravitational circulation. A linear function negatively relates estuarine flushing to the tidal amplitudes near the mouth of the estuary, whereas a power-law function relates estuarine flushing to the freshwater inflow near the head. In addition, strong stratification induced by freshwater discharge and small tidal amplitude exerts dominant control to reduce the estuarine flushing in the central and upper regions of the estuary during a neap tide.