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The understanding of physical processes over submerged reefs represents an important ongoing research topic when considering wave energy dissipation and coastal protection that these environments provide. Detailed analyses are required to assess wave damping based on the contribution of reef roughness and wave breaking. For this purpose, the CFD (computational fluid dynamics) toolbox OpenFOAM® is applied to simulate the wave energy dissipation process over reefs with explicit accounting for the complexities of coral shape instead of commonly applied parameterized approaches for bottom roughness and wave breaking. Model validation was performed through comparison with field measurements over a reef profile of Tesoro Island in the Colombian Caribbean. Quantitative analysis of wave damping caused by wave breaking and reef roughness was conducted for (1) moderate and extreme wave conditions, (2) smooth and rough seabed configurations and (3) changes in the water depth over the reef crest. Wave height attenuation is found to vary along the reef profile reaching differences of up to 55% between smooth and rough reef surface scenarios, particularly for moderate wave conditions. Wave breaking, high turbulent flows and detachment of undertow currents are among the reef roughness effects on hydrodynamics. The fore-reef terrace and the reef crest are identified as the most critical zones where dissipation takes place. Wave breaking from rough seabeds provides a global wave attenuation of 75.4–94.8%, with the reef roughness alone accounting for ~ 4–14%. Under extreme wave height scenarios, the wave damping from reef roughness is not significant. Further predictions regarding roughness effects on the reef hydrodynamics, wave set-up and undertow currents for moderate and extreme wave climate conditions are also shown. Directions for future research using CFD are presented to address limitations that arise from the limited span-wise domain in our approach that prevents development of large lateral coherent structures. Inglés