Bangladesh, one of the most disaster-prone countries in the world, has a dynamic delta with 123 polders protected by earthen dikes. Cyclone induced storm surges cause severe damages to these polders by overtopping and breaching the dikes. Nineteen major tropical storms hit the coast in last 50 years and storm intensity is predicted to increase due to climate change. The present paper presents an investigation of the inundation pattern in a protected area behind dikes due to floods caused by storm surges and identifies possible critical locations of dike breaches. Polder 48 in the coastal region, also known as Kuakata, was selected as the study area. A HEC-RAS 1D–2D inundation model was developed to simulate inundation under different scenarios. Tidal variations, angle of the cyclone at landfall, different dike breach locations, geometrical properties of the breach, breach propagation time and the sea level rise due to climate change according to the fifth assessment report (AR5) of Intergovernmental Panel on Climate Change (IPCC) were combined to develop the scenarios. The critical location of the dike breach was identified by comparing the three worst cases of the developed scenarios. Generated flood risk maps corresponding to the breaching at the critical location indicated that settlements adjacent to the canals face higher risk. The probabilistic flood map (PFM) calculated from the results of all the developed scenarios indicated the need of appropriate land use zoning to minimize the vulnerability to flooding. The developed model can be applied to generate location based flood forecasting, identify critical locations of the dike to reduce the risk from flooding and to study the effect of climate change.