This study estimates a heat budget of the Great Barrier Reef and Coral Sea off the northeast coast of Australia. The air-sea heat fluxes and ocean advective heat transport were examined for the present and future so as to determine the relative roles of the atmosphere and ocean in creating anomalies in oceanic heat content and sea surface temperatures. These findings are extended over a longer time period to ascertain the likely future climate for the region using outputs from various coupled ocean-atmosphere general circulation models, and a downscaled general circulation model over the Australasian region. These were used to assess past, current and future climate conditions, the factors responsible for maintaining these conditions and the processes driving changes in climate. This study shows that sea surface temperatures, and to a lesser extent net surface heat fluxes display increasing trends during the 20th century and are very likely to continue to increase in the 21st century, with rates 2 to 4 times higher, increasing thermal stress on the ecosystems such as coral bleaching, leaving cooling by oceanic dynamical mechanism as a possible process to ameliorate these effects.