Sea level rise and intensified storm surges due to climate change are assumed to increase inundation risks in coastal areas. While climate change adaptation policies are being developed in Japan, the long-term changes in inundation risk have not yet been quantified. This study estimated potential inundation risk areas by considering sea level rise and future population changes for three major bays in Japan under different SSP scenarios. Additionally, storm surge simulations for Typhoon Jebi in Osaka Bay were conducted under high tide conditions, incorporating sea level rise, to estimate future changes in the inundated area and the storm surge-affected population. The results indicated that the affected population was greater than that of changes in hazard intensity. A significant increase in impacts after 2020 was observed only under the high emission scenario with SSP5–8.5 in Tokyo Bay. This analysis highlighted that differences between scenarios for the population in high-risk areas concerning storm surges become more significant after 2060.