This dataset consists of physics-based XBeach Non-hydrostatic hydrodynamic models input files used to study how coral reef restoration affects waves and wave-driven water levels over coral reefs, and the resulting wave-driven runup on the adjacent shoreline. Coral reefs are effective natural coastal flood barriers that protect adjacent communities. Coral degradation compromises the coastal protection value of reefs while also reducing their other ecosystem services, making them a target for restoration. Here we provide a physics-based evaluation of how coral restoration can reduce coastal flooding for various types of reefs. These input files accompany the modeling conducted for the following publication: Roelvink, F.E., Storlazzi, C.D., van Dongeren, A.R., and Pearson, S.G., 2021, Coral reef restorations can be optimized to reduce coastal flooding hazards: Frontiers in Marine Science, https://doi.org/10.3389/fmars.2021.653945.