Coastal cities are growing at a very rapid pace, in terms of both population and physical assets, and great uncertainty surrounds the future evolution of flood due to storm surge and sea-level rise. Storms are a major cause of loss of human life and property in many coastal cities around the world. It is therefore essential to accurately predict the impact of storm surges to assess an area’s flood risk and plan to minimize it. Historical records of storms are too short and too sparse to support reliable statistical predictions of storm surge levels; thus, numerical analysis is used for simulating and predicting flooding in coastal areas. In recent years, improvements in the understanding of the physics of storm surge processes have led to the development of computationally intense hydrodynamic models capable of estimating storm surge elevations. In this study, an attempt is made to assess the impact of storm surges in the coastal region by integrating numerical hydrodynamic and wave model with GIS. The study concentrated on the coastal panchayats of Alappuzha district namely, Arattupuzha, Thrikkunnapuzha, Purakkadu and Ambalapuzha south. A numerical model using MIKE21 was developed for the study area to simulate storm surges by integrating hydrodynamic and wave model. The coupled model is calibrated by optimizing the parameters and validated based on observed data. The performance of the model is assessed using RMSE, RRMSE and MRE where the developed model and the model results were found to be in good agreement with the observed data. The developed model was then used to simulate storm surge and wave condition for five different storm scenarios. From the results of the simulations, it is found that the surge heights are dependent of high wind speed and astronomical tide elevation during the period of occurrence. The high intensity rainfall has also an effect on the water level rise during the storm surges. The coastal inundation extent under different storm scenarios were also mapped using the results from the storm surge simulations and the severity of coastal inundation during storm surges were also assessed.