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Many low‐elevation, coral reef‐lined, tropical coasts are vulnerable to the effects of climate change, sea level rise, and wave‐induced flooding. The considerable morphological diversity of these coasts and the variability of the hydrodynamic forcing that they are exposed to make predicting wave‐induced flooding a challenge. 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. It was found that, in order to accurately predict flooding hazards, water depth over the reef flat, incident wave conditions, and reef flat width are the most essential factors, whereas other factors such as beach slope and bed friction due to the presence or absence of corals are less important. 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.