This study assesses the coastal flooding risks to tunnels in Manhattan, New York, under various scenarios. The study uses GIS-based inundation modeling to evaluate the impact of storm surges similar to Superstorm Sandy on future sea levels. Five scenarios are analyzed: a current baseline for 2010 and four future projections for 2100 using RCP 4.5 and 8.5, with and without enhanced Antarctic Ice Sheet contributions. Future DEMs and flood depth grids are generated using the IDW interpolation technique. Based on these results, the flood heights at tunnel exits and entrances are estimated and then compared to the tunnel heights to assess the flooding risk. In the most extreme scenario, by 2100, 75% of studied tunnel entrances and exits will be located below sea level, causing inundations of 1.57-10.41 meters, depending on the location. Consequently, the vulnerability of these tunnels to storm surges will become more severe in future climate scenarios.