Waves generated by tropical cyclones and tsunamis cause various impacts such as coastal erosion and damage to infrastructure. The intensity of tropical cyclones will probably increase in the near future as a result of global warming; therefore, predicting the likely impacts of these storms is a prime concern. Boulder deposits are one of the key proxies that assist our understanding of previous tropical cyclones and tsunamis, and are important if we are to accurately project their future impacts. In December 2012, Typhoon Bopha hit the Palau Islands and many boulders were probably deposited on the east coast of Babeldaob Island during the event. This area is one of the few locations where it is possible to distinguish between deposits that were generated by tropical cyclone waves and tsunamis. This study records the distribution of boulders from the shore to the reef crest at Melekeok reef on Babeldaob Island and evaluates the relationship between the movement of boulders and the hydraulic forces generated by the waves using a hydrodynamic model and wave calculations. In addition, this study projects the coastal impacts of tropical cyclone waves in the near future. Many boulders have been deposited on the reef crest within 100 m of the reef edge, and the maximum weight of the boulders is 2.2 tons. The boulders are composed of massive corals (e.g., Platygyra) and they originated from the upper reef slope. The results of the hydrodynamic modeling indicate that these boulders were transported and deposited by the waves generated by Typhoon Bopha (significant wave height = 8.7 m) or TCs with a similar intensity of Typhoon Bopha. Moreover, there are no boulder deposits at the shore, which implies that the reef has not been affected by tsunamis. Even if one or more tsunamis have inundated the reef, the associated hydraulic forces appear to have been lower than those of Typhoon Bopha. These findings indicate that Typhoon Bopha has probably generated the most intense wave event in recent times. However, it is likely that tropical cyclones more intense than Typhoon Bopha will affect the reef in the near future as the climate continues to warm through the 21st century. Consequently, the study site will probably face an increased risk of coastal erosion and destruction of property, if no plans are developed to reduce and manage such impacts.