A set of physics-based XBeach Non-hydrostatic hydrodynamic model simulations (with input files here included) were used to evaluate how varying carbonate budgets, and thus coral reef accretion and degradation, affect alongshore variations in wave-driven water levels along the adjacent shoreline of Buck Island Reef National Monument (BUIS) for a number of sea-level rise scenarios, specifically during extreme wave conditions when the risk for coastal flooding and the resulting impact to coastal communities is greatest. These input files accompany the modeling conducted for the following publication: Toth, L.T., Storlazzi, C.D., Kuffner, I.B., Quataert, E., Reyns, J., McCall, R.T., Stathakopoulos, A., Hillis-Starr, Z., Holloway, N.H., Ewen, K.A., Pollock, C.G., Code, T., and Aronson, R.B., 2023, The potential for coral reef restoration to mitigate coastal flooding as sea levels rise: Nature Communications, v. 14, https://doi.org/10.1038/s41467-023-37858-2.