Unlike inundation from a tsunami, inundation originating from a tropical cyclone is rather complex since it is usually accompanied by torrential rain. Runoff in the vicinity of an estuarine outlet may thus incur additional inundation damage. In this study, a modeling system is proposed that considers the river discharge effect in addition to tides and surges to enhance the modeling accuracy of storm-induced inundation in coastal areas. The hydrodynamic model (Delft3D) and hydrological model (HEC-HMS) were coupled to account for all the flooding drivers, such as tides, storm surges, river discharges, and their interactions. In the coupled model, Delft3D was responsible for tidal and storm-induced surging motions, while HEC-HMS was used to calculate the river discharge at the downstream outlet of basins. Typhoon Maemi, which caused severe inundation damage to the Korean peninsula in 2003, was simulated by the model with a focus on the localized inundation process. The increase in inundation risk caused by river discharge was of particular interest and was assessed through a comparison of two different cases: Case ST (Storm-Tide) and Case STR (Storm-Tide-Riverine flow). The results clearly show that the case considering the rainfall-runoff process in the storm surge simulation outperforms that in which storm surge is not considered. A further detailed investigation of the inundation depth and coverage of both cases revealed several findings. The proposed model is expected to be of great aid in producing the flood hazard mapping with enhanced accuracy.