Although global warming is leading to more frequent mass coral bleaching events worldwide, parts of the Great Barrier Reef (GBR) have consistently escaped severe coral bleaching. Modeling and satellite observations show that climate refugia are created by the upwelling of cooler water to the surface through the interactions of tides and currents with dense reef structures. Here, we use a high-resolution nested regional ocean model to investigate the future status of two relatively large refugia. On the basis of model projections under a high-emission scenario, we find that the upwelling mechanisms will stay active in a warming climate, and these regions are likely to remain approximately more than 1°C cooler than surrounding waters until at least into the 2080s, providing thermal relief to corals. Identification and protection of these refugia may help facilitate reef survival and related biodiversity preservation by allowing their corals time to acclimatize and adapt and ultimately provide source populations to replenish the rest of the reef.