Effects of combined rising sea temperature and increasing sea level on coral reefs, both factors associated with global warming, have rarely been addressed. In this ~40 y study of shallow reefs in the eastern Indian Ocean, we show that a rising relative sea level, currently estimated at ~11 mm y−1, has not only promoted coral cover but also has potential to limit damaging effects of thermally-induced bleaching. In 2010 the region experienced the most severe bleaching on record with corals subject to sea temperatures of >31 °C for 7 weeks. While the reef flats studied have a common aspect and are dominated by a similar suite of coral species, there was considerable spatial variation in their bleaching response which corresponded with reef-flat depth. Greatest loss of coral cover and community structure disruption occurred on the shallowest reef flats. Damage was less severe on the deepest reef flat where corals were subject to less aerial exposure, rapid flushing and longer submergence in turbid waters. Recovery of the most damaged sites took only ~8 y. While future trajectories of these resilient reefs will depend on sea-level anomalies, and frequency of extreme bleaching the positive role of rising sea level should not be under-estimated.