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. Reefs and sand dunes are critical morphological features providingnatural coastal protection. Reefs dissipate around 90  % ofthe incident wave energy through wave breaking, whereas sand dunesprovide the final natural barrier against coastal flooding. The stormimpact on coastal areas with these features depends on the relativeelevation of the extreme water levels with respect to the sand dunemorphology. However, despite the importance of barrier reefs and dunesin coastal protection, poor management practices have degraded theseecosystems, increasing their vulnerability to coastal flooding. Thepresent study aims to theoretically investigate the role of thereef–dune system in coastal protection under current climaticconditions at Puerto Morelos, located in the Mexican Caribbean Sea,using a widely validated nonlinear non-hydrostatic numerical model(SWASH). Wave hindcast information, tidal level, and a measured beachprofile of the reef–dune system in Puerto Morelos are employed toestimate extreme runup and the storm impact scale for current andtheoretical scenarios. The numerical results show the importance ofincluding the storm surge when predicting extreme water levels andalso show that ecosystem degradation has important implications forcoastal protection against storms with return periods of less than10 years. The latter highlights the importance of conservation of thesystem as a mitigation measure to decrease coastal vulnerability andinfrastructure losses in coastal areas in the short to mediumterm. Furthermore, the results are used to evaluate the applicabilityof runup parameterisations for beaches to reef environments. Numericalanalysis of runup dynamics suggests that runup parameterisations forreef environments can be improved by including the fore reefslope. Therefore, future research to develop runup parameterisationsincorporating reef geometry features (e.g. reef crest elevation, reeflagoon width, fore reef slope) is warranted.

The role of the reef–dune system in coastal protection in Puerto Morelos (Mexico)