Coral reefs in the Great Barrier Reef (GBR) are subject to disturbances due to increasing frequency and intensity of cyclones with the changing climate. The wave energy of the cyclonic waves impact the corals, damaging them leading to break down of the coral framework. The generated coral rubble are destabilized due to hydrodynamic forces that damage the new coral recruits, thus hindering reef recovery. As the reef rubble consolidation and stabilization takes years to decades, the reefs in the GBR continue to shift to rubble dominated state, and it is necessary to understand the hydrodynamic processes responsible for rubble generation and mobilization. In this study, xBeach hydrodynamic numerical model is implemented to simulate everyday to cyclonic wave conditions over Heron Island and reef region, to understand wave transformation over the reef and predict coral breakage as well as rubble motion. The significant wave heights for these simulations ranged from 0.25m to 11m. The hydrodynamic model outputs such as significant wave heights and velocities are used to predict coral breakage based on a prediction model in which the calculated maximum bending stress due to fluid drag forces on the coral colonies are compared with the coral’s mechanical strength obtained from field samples and earlier literature. A lookup table of coral breakage fraction for different flow velocities was developed based on this model. The rubble motion model is based on calculating the probability of wave velocity exceeding a certain threshold value required for motion (obtained from field and laboratory studies) by integrating the probability of the velocities across a range of wave height and period joint distribution for a given significant wave height, peak period and water depth. Maps of coral breakage and rubble motion on the Heron reef are produced for identification of locations of reef recovery risks.