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Coral reefs cover approximately 0.10 to 0.25% of the marine environment and yet are home to around 25% of marine species and support the livelihoods of more than 500 million people. They face a wide range of threats, with the impact of global warming gaining most attention due to its frequently claimed causal link to coral bleaching. Herewe review a decade of research into themicrometeorology ofHeron Reef, a lagoonal platform coral reef in the southern Great Barrier Reef, Australia. Using novel pontoon-mounted eddy covariance systems, we show that often > 80% of net radiation is partitioned into heating the water overlying the reef, the reef benthos, and substrate. Significant spatial variability in energy and trace gas exchanges occurs over the reef in response to different geomorphic and hydrodynamic conditions. Synoptic weather patterns that bring light winds, clear skies, and high humidity, result in reef scale meteorology that appears to have a greater influence on coral bleaching events than the background oceanic warming trend. The reef develops its own convective internal boundary layer, with potential to influence cloud development and therefore the surface energy balance. Knowledge of such local effects is lacking, so it is recommended that future research is needed into reef scale processes and how they interact with larger-scale forcing.