This study aims to extend the existing climate-change-induced flood mitigation research. We introduce an at-risk network to evaluate optimal cost–benefit strategies for creating dikes and levees to mitigate flood hazard over multiple years. Our proposed model includes the expected flood costs, estimated using possible climate-change-induced sea-level states throughout the planning horizon, and the investment costs for developing dikes and levees via land elevations across the at-risk network. Further, given the limitations on infrastructure investment, our model incorporates a budget constraint. The problem is modeled as a multistage stochastic program with recourse that minimizes overall expected costs over the planning horizon. Exploiting open-source and freely accessible data sets, the flood risk mitigation model elaborated here can be applied to most urban coastal situations due to its general nature. Using Boston as a case study, our proposed method resulted in a cost reduction of as much as 92.2%, with an average of 63.2%, compared to a “do nothing” strategy in a simulation-based experiment. Under a high sea-level rise scenario, the average cost savings observed by implementing the solution suggested by our model could be even 15% higher. This proposed approach offers decision-makers a tool to frequently assess the costs and risks faced by their cities enabling them to effectively mitigate the potential flooding risks.