Most tropical corals live in symbiosis with Symbiodiniaceae algae whose photosynthetic production of oxygen (O₂) may lead to excess O₂ in the diffusive boundary layer (DBL) above the coral surface. When flow is low, cilia-induced mixing of the coral DBL is vital to remove excess O₂ and prevent oxidative stress that may lead to coral bleaching and mortality. Here, we combined particle image velocimetry using O₂-sensitive nanoparticles (sensPIV) with chlorophyll (Chla)-sensitive hyperspectral imaging to visualize the microscale distribution and dynamics of ciliary flows and O₂ in the coral DBL in relation to the distribution of Symbiodiniaceae Chla in the tissue of the reef building coral, Porites lutea. Curiously, we found an inverse relation between O₂ in the DBL and Chla in the underlying tissue, with patches of high O₂ in the DBL above low Chla in the underlying tissue surrounding the polyp mouth areas and pockets of low O₂ concentrations in the DBL above high Chla in the coenosarc tissue connecting neighboring polyps. The spatial segregation of Chla and O₂ is related to ciliary-induced flows, causing a lateral redistribution of O₂ in the DBL. In a 2D transport-reaction model of the coral DBL, we show that the enhanced O₂ transport allocates parts of the O₂ surplus to areas containing less chla, which minimizes oxidative stress. Cilary flows thus confer a spatially complex mass transfer in the coral DBL, which may play an important role in mitigating oxidative stress and bleaching in corals.