Coral reefs are a natural habitat for many species, as well as being of high economic and touristic significance. However, they represent an extremely sensitive ecosystem with a narrow ecological limit: prolonged high temperatures can lead to bleaching, in which corals expel their symbiotic algae and eventually corals will degrade and die. This work investigates the potential threat of rising temperatures to coral reefs in Southeast Asian Seas through a case study of the UNESCO Cu Lao Cham – Hoi An Biosphere Reserve. We assessed the risk caused by both rising sea surface temperature (SST) and occurrence of more extreme El Niño events. Using outputs from a regionally-downscaled climate model, we found that by the decades 2041-2050 and 2051-2060, whether with RCP 4.5 or RCP 8.5, the environmental temperature will change beyond the coral capacity threshold. Of particular concern is RCP 8.5, where the number of weeks per decade in which SST exceeds the threshold of coral reef bleaching is up to 55, compared to 0 at the beginning of the century. As well, the El Niño phenomenon often heats up waters to abnormally high temperatures in Cu Lao Cham and, using polynomial extrapolation, it is projected to rise even further. Consequently, the combination of climate change and El Niño will cause abnormal increases in the seawater environment beyond the coral resistance threshold, leading to degradation of this internationally important site.