The removal of reservoir silt and the restoration of existing reservoir capacities through land excavation and hydraulic sediment flushing have become necessary. Hydraulic sediment flushing discharge changes flow and sediment conditions of the downstream river channel. In the Tamsui River estuary in Taiwan, sediment flushing from the Shihmen reservoir upstream has potential impacts on the morphology of the navigation channels and the adjacent coasts. This study employed a validated coastal and estuarine processes model to investigate: (1) the influence of sediment flushing and tidal levels on morphological changes during flood and flushing‐discharge operations of the reservoir, and (2) the differences in morphological changes on the estuary between monsoon and typhoon seasons. The prediction of the morphological changes was carried out by simulating hydrodynamic and morphodynamic processes under multi‐year synthetic conditions combined by northeast monsoon and three historical typhoon events. The simulation results reveal that during the operation of sediment flushing when the peak discharge of river flood flow reaches the estuary section at ebb tides, more sediment can be transported to the open sea than that at flood tides. Additionally, the nature reserve area on the left bank of the estuary is eroded during monsoon and silted in typhoon seasons.