In this study, an integrated coastal process model was applied to assess impact of coastal flooding and sedimentation in an estuary in Taiwan and to evaluate performance of proposed engineering plans for flood prevention and sedimentation management. This in-situ validated model was used to simulate and predict hydrodynamic processes and morphological changes induced by multiple hydrological forcing such as river flood flows, waves, tides, and storms surges from rivers to the estuary and its adjacent coasts. Simulation results quantified coastal flooding risks, erosions, sedimentation, and channel refilling. Predicted dynamic responses to typhoons and monsoons were utilized for identifying the most effective engineering plan to reshape the geometry of the estuary. After the selected engineering plan was accomplished, this model was applied again to further predict morphological changes in the newly-developed estuary. This paper demonstrates effectiveness of a simulation-based coastal and estuary planning approach to manage flood and sedimentation driven by complex physical processes from river flows, waves, tides, and sediment transport.