By means of the physical process-based modeling approache to computing coastal and estuarine hydrodynamic and morphodynamic processes, an integrated model system was developed to simulate tides, waves, currents, winds, sediment transport, and morphological changes in coastal and estuarine regions. This paper presents an overview of this integrated morphological process modeling system consisting of modules for simulating random wave deformations, tidal and shortwave-induced currents, sediment transport and morphological changes. The individual modules included in the integrated model system were validated by simulating hydrodynamic and morphodynamic processes in laboratory experiements and field study cases. An example for model application to an estuary is presented to demonstrate the model's effectiveness in simulating comprehensive impacts of combined storm waves, typhoons (or hurricanes), river floods, sediment transport, and morphological changes in its coastal and estuarine area. This modeling system provides engineers and researchers with an efficient and effective numerical software package to facilitate better coastal erosion protection, flood and inundation prevention, coastal strom water management and infrastructure protection against hazardous storms, typhoons, and hurricanes.