Using nested ocean models, we dynamically downscaled climate model outputs for the Great Barrier Reef (GBR) under a very-high-emission scenario. Our results show that upwelling of cold water by currents, waves and tides producing climate refugia for reefs in the Northern and Southern GBR in the current climate will continue to be effective in the future warming climate. Upwelling reduces the effect of marine heat waves on corals, with the sea surface temperature in the upwelling region cooler than surrounding waters by more than 1 degree. Identification and protection of these refugia may help facilitate reef survival and related biodiversity by allowing corals time to acclimatize and adapt, and provide source populations to replenish the rest of the reef.