[1] Coral reefs are thought to face significant threat from global warming due to increased water temperatures and ocean acidity. However, research into the surface energy balance of coral reefs and their associated micrometeorology is rare. Here we present, through a case study approach, the first direct in situ measurements of the surface energy balance of Heron Reef, a small platform coral reef in the southern Great Barrier Reef, Australia. Surface energy exchanges were measured using the eddy covariance method and show that during winter and spring an estimated 80-98% of net radiation goes into heating of the water overlaying the reef and reef substrate. As a result, cloud cover is considered the dominant control on heating of the reef flat environment. Change in cloud cover may therefore significantly affect the thermal environment of coral reefs and their ecology. Sensible and latent heat fluxes reached their highest values during wintertime advection of dry and cool continental air blowing from mainland Australia. This resulted in a net loss of energy from the reef flat and a decreasing trend in water temperature. Turbulent fluxes otherwise remained small, with sensible heat flux often close to zero. Results indicate that coral reefs may act as heat sinks during winter and as heat sources during spring, thereby affecting local water and atmosphere heat budgets and associated thermodynamics.