Sea level rise predictions have motivated research towards the protection of shoreline infrastructures, including transportation systems. Transportation network interactions in cases of inundation can lead to severe disruptions that cause capacity and accessibility reduction and thus considerable delays, especially due to congestion feedback, because congestion occurring due to an inundated link or a link that becomes isolated through inundation of one of its nodes can lead to delays in other parts of the network, due to queue spillback or traffic rerouting. This paper describes a decision tool to support infrastructure protection planning against sea level rise. A simulation-based optimization model is designed to minimize delays occurring in a transportation system under inundation. The model considers budget constraints, hydrodynamic interactions within the shoreline, as well as traffic assignment in the network. The case study focuses on San Francisco Bay area, for a 0.5 m sea level rise that is expected in 2054 and may increase highway users’ travel time by 37%. The results show that the optimal strategies vary according to the available budget, and that there exist relatively critical shorelines to protect in order to reduce the traffic disruptions. We anticipate our research to provide a general framework for transportation infrastructure protection planning against sea level rises.