A coastal and estuarine model has been extensively validated by simulating morphodynamic responses to long-term hydrological conditions including typhoons, storm waves, winds, and river floods occurred in an estuary. The computed morphological changes over several years are in good agreement with the in situ bathymetry measurements. The numerical results also revealed complex flow patterns and morphological changes in the estuary, e.g., bank overflow and coastal inundation, erosion/deposition, as well as breaching of river mouth sand bar. These results are important to understanding of sediment transport and morphodynamic processes in the estuary especially due to storms, tides, and floods. This validated numerical model is, therefore, capable of assisting engineers and researchers to achieve better long-term coastal flood management and infrastructure design against various complex hydrological conditions in coasts and estuaries.