This paper presents a practical engineering application of an integrated coastal model in coastal and estuarine planning for flood and erosion protection against hazardous hydrological forcing such as river floods, storm surges, waves, and high tides in an estuary in Taiwan. It demonstrates the advancement of the integrated modeling system to simulate hydrodynamic and morphodynamic processes in the estuarine area including rivers and adjacent coastal zones in responses to combined tides, waves, river flood, and winds. In order to identify the best engineering plan for the purpose of flood prevention and erosion protection, the integrated coastal models are applied to evaluate a number of engineering plans by simulating long-term variations of hydrodynamic and morphodynamic processes under a hypothetical storm-monsoon event which contains a 100-year storm and a three-month-long monsoon. Numerical results on flood water stages and morphological changes enable engineers to find the most desirable engineering plan for protecting the estuarine area from flood inundation and erosions. The integrated modeling system provides a comprehensive assessment tool for coastal and estuarine planning in complex hydrological and geomorphologic conditions.