Floods are one of the extreme events and widespread natural disasters that significantly affect the civil infrastructure and livelihoods of people. Recently, climate change has significantly altered the rainfall pattern and increased flood events worldwide, especially in India. Therefore, it has become essential to map potential flood inundation regions for various future extreme events to develop appropriate flood mitigation and management strategies. This study aims to develop flood inundation maps for different return periods under climate change scenarios for the Chaliyar basin, Kerala. The Hydrologic Engineering Center-Hydrologic Modelling System model was used to simulate streamflow under SSP2-4.5 and SSP5-8.5 scenarios. Later, flood inundation maps were developed for different return periods using the Hydrologic Engineering Center-River Analysis System model. It was observed that for the near future (2031–2040) and far future (2071–2080), simulated streamflow is higher for SSP5-8.5. However, the mid-future (2051–2060) resulted in a higher streamflow for SSP2-4.5 than the SSP5-8.5 scenario. A maximum of 19.52 m of water surface elevation occurred at Kizhupparamba during mid-future for SSP2-4.5, followed by 18.38 m of water surface elevation at Cheekode during the near future for SSP5-8.5, for 100-year return period events. This study showed that hydrologic and hydraulic models could be effectively combined for mapping the flood inundation areas.