Global warming and ocean acidification (OA) have increased over the last decades, affecting coral reefs in various ways. Temperature stress may disrupt the photosymbiosis between corals and their microalgal symbionts and lead to photoinhibition, bleaching and mortality of the corals. Decreases in pH and aragonite saturation may slow coral calcification and growth. Coral reefs may cope with global warming and OA both, on the organismal level, where adaptive bleaching may foster coral associations with heat-tolerant Symbiodinium clades, and on the ecosystem level, where coral communities may become dominated by less bleaching and OA-susceptible species. Here, I show that reef environments displaying high natural fluctuations in temperature and pH due to upwelling by internal waves are important refuges for corals in a changing world. Desert-enclosed shallow water reefs like the ones occuring in the Persian Gulf displaying large diurnal and seasonal variations in environmental conditions may harbour important preadaptations by corals to a changing climate.