In this study, we conducted storm surge inundation modeling considering estuarine discharge from heavy rainfall during storm events. As the tropical cyclone involves storm surge and heavy rainfall, it causes more complex damages in low-lying coastal city with the estuarine discharge. We combined Delft-3D, hydrodynamics model with HEC-HMS, hydrology model in order to simulate storm surge inundation in low-lying coastal city during a tropical cyclone. In the coupled model, we calculated runoff caused by rainfall using HEC-HMS and utilized it as river boundary condition. Also, we considered tide motion using TPXO 7.2 model and calculated typhoon's wind field with Holland's model. As a result, during the tropical cyclone there wasn't any significant difference in sea level rise. However, the inclusion of river flow resulted in large difference with respect to inundation. In addition, we can confirm that maximum inundation depth and inundation area calculated by the model considering river flow are in more agreement with real observation. From the results, we can conclude that maximum inundation depth and inundation area due to tropical cyclone are significantly influenced by river flow in coastal cities with river inflow.