A process-based wave-resolving hydrodynamic model (XBeach Non-Hydrostatic, ‘XBNH’) was used to create a large synthetic database for use in a “Bayesian Estimator for Wave Attack in Reef Environments” (BEWARE), relating incident hydrodynamics and coral reef geomorphology to coastal flooding hazards on reef-lined coasts. Building on previous work, BEWARE improves system understanding of reef hydrodynamics by examining the intrinsic reef and extrinsic forcing factors controlling runup and flooding on reef-lined coasts. The Bayesian estimator has high predictive skill for the XBNH model outputs that are flooding indicators, and was validated for a number of available field cases. BEWARE is a potentially powerful tool for use in early warning systems or risk assessment studies, and can be used to make projections about how wave-induced flooding on coral reef-lined coasts may change due to climate change. These data accompany the following publication: Pearson, S.G., Storlazzi, C.D., van Dongeren, A.R., Tissier, M.F.S., and Reniers, A.J.H.M., 2017, A Bayesian-based system to assess wave-driven flooding hazards on coral reef-lined coasts: Journal of Geophysical Research—Oceans, https://doi.org/10.1002/2017JC013204.