Strong and sustained southerly winds that brought heavy rain to much of southeast Queensland in June and July exacerbated the chilly conditions for coral exposed at low tide and weakened the algae on the coral needed to keep it healthy.
Professor Hoegh-Guldberg said the comfort zone for coral was between 19C and 27C but temperatures had fallen to 8C.
While bleaching from extreme heat affects entire reefs, the cold bleaching appears to be isolated to the tips of wide areas of coral exposed to the chill.
Professor Hoegh-Guldberg said the extreme variation in temperature might be more common as climate change caused hotter summers and colder winters.
CSIRO oceanographer David Griffin said the only noticeably cold currents were further south, around Fraser Island, suggesting water was being cooled at the surface by the air temperature.