Franklin, G.L., Mariño-Tapia, I. and Torres-Freyermuth, A., 2013. Effects of reef roughness on wave setup and surf zone currents.Circulation in reef systems controls an important number of key processes, such as the transport and dispersion of larvae, nutrients, and sediments. In fringing reef systems, where a shallow lagoon backs onto the reef crest, circulation appears to be dominated by wave breaking. Despite the identified importance of wave driven flows within reef systems, there is a lack of detailed knowledge on these processes within the surf zone of reef crests and the effects reef roughness has on these flows. A numerical study, using two-dimensional (2DV) simulations, was carried out in order to improve the understanding of wave-driven flows in the surf zone of a fringing reef. The model used is Cornell Breaking Wave and Structures (COBRAS), which solves the Reynolds-Averaged Navier-Stokes (RANS) equations with a turbulence closure scheme. The effect of different reef roughness on wave height, wave setup, infragravity waves and mean flows was studied. Model results revealed that wave setup increases significantly (~22%) with increasing bed roughness, consistent with prior studies on sandy beaches. Furthermore, cross-shore velocity structure is heavily affected by bed roughness. The latter implies that the coral reef flattening trend observed world-wide could result in a decrease in the circulation within the lagoon with important implications for reef health.