Understanding what causes water to get get extremely hot around coral is a physics problem. It is an example of where it is essential to understand far more than just biology to understand the coral reefs. The physics of the absorption of sunlight that heats the water, and evaporation from the surface that cools the surface, is especially relevant. Most of the sunlight is absorbed in the top few metres of the water, with about 13 percent of the sunlight being absorbed in the top millimetre.[i] Without some sort of cooling mechanism, the water at the surface millimetre or two would boil in approximately one hour! Evaporation cools the surface in the same way as evaporation of sweat on human skin cools us when we are hot. In addition, cooling occurs due to infra-red radiation emitted from the top few microns of the surface. Finally, waves and currents stir the water and mix the hot water downwards, and the deeper cool water upwards to the surface.
Two things are necessary to get unusually hot water – low wind and no cloud. Low wind speed has two effects. Firstly, it means there are no waves so the cool water at depth is not mixed upward to the surface. Secondly, low wind means low evaporation so the surface cooling is reduced. The effect of no clouds is more obvious; it means that the sun shines with peak power giving maximum heating. The net result is that water near the surface becomes a few degrees hotter than normally under these circumstances.
El Nino years are particularly likely to produce conditions of low wind and low cloud. 1998 and 2016 were El Nino years. But in any particular location there is always a possibility that the water can get a few degrees above average and the coral will bleach.
[i] Mobasheri, M.R. (1995). Heat transfer in the upper layer of the ocean with application to the satellite sea surface temperature (SST) measurement. PhD Thesis.
Great Barrier Reef Science Commentary 