Coastal resilience has become a pressing global issue due to the growing vulnerability of coastlines to the effects of climate change. Nature-based solutions have emerged as a promising approach to coastal protection to not only enhance coastal resilience, but also restore critical ecosystems. Coral reef restoration has the potential to provide ecosystem services benefits; however, there are still key uncertainties in linking restoration design to reductions in coastal flood hazard under current and future climate conditions. In this study, we applied one-dimensional and two-dimensional numerical coastal engineering models, calibrated and validated using field data, to evaluate the effectiveness of coral restoration scenarios on coastal waves, water levels, and flooding along the coast of San Juan, Puerto Rico, U.S.A. Model results indicate a small reduction in maximum water levels under the proposed restoration scenarios. This underscores the importance of these endeavors, not only for ecological preservation but also for preventing further reef deterioration. Such preservation is essential for mitigating the increased coastal risks anticipated in the future. Results from this study provide information to guide policymakers and coastal managers in making informed decisions on viable restoration project design options. By systematically evaluating how restoration location impacts coastal flood hazards, communities can develop and implement proactive strategies to mitigate flood-related risk. In addition, by restoring coral reefs, communities can contribute to environmental preservation while ensuring sustainable development and protection of coastal environments.