Coastal inundation due to wave overtopping coastal structures and storm surges often causes serious damage and danger to the population of Taiwan. Ascertaining the areas that are prone to coastal inundation is essential to provide countermeasures for mitigating the problem. Simulations without precipitation are examined in this study since overtopping has been determined to be a controlling factor in coastal flooding. We present scenarios for the simulation of coastal flooding with a unified wind wave and hydrological watershed model. The eastern coastal areas in Taiwan are selected as the study area. Simulations show that the resulting waves and tidal levels, generated by the Rankin-Vortex model and wind wave calculations, can be successfully obtained from the input data during wave overtopping simulations. A watershed model, WASH123D, was then employed for surface routing. The simulations indicate that the low-lying Yilan River and Dezikou Stream drainage systems were among the primary areas subject to inundation. Extensive inundation along both sides of the river banks was obtained in the case of extreme overtopping events. Coastal inundation could occur between the estuary of the Meilun Stream and most of the Nan-Bai-Bin areas in Hualien City. Calculations showed that more croplands flooded than did residential regions. No further damage to the upland of Hualien City was identified. The remaining study sites, Sinchen Township, Taitung City and Taimali Township, would only be slightly affected by seawater run-ups. Inundations caused by overtopping under extreme circumstances only affected the coast with almost trifling influence inland.