The thermal microenvironment of corals and the thermal effects of changing flow and radiation are critical to understanding heat-induced coral bleaching, a stress response resulting from the destruction of the symbiosis between corals and their photosynthetic microalgae. Temperature microsensor measurements at the surface of illuminated stony corals with uneven surface topography (Leptastrea purpurea and Platygyra sinensis) revealed millimetre-scale variations in surface temperature and thermal boundary layer (TBL) that may help understand the patchy nature of coral bleaching within single colonies. The effect of water flow on the thermal microenvironment was investigated in hemispherical and branching corals (Porites lobata and Stylophora pistillata, respectively) in a flow chamber experiment. For both coral types, the thickness of the TBL decreased exponentially from 2.5 mm at quasi-stagnant flow (0.3 cm s(-1)), to 1 mm at 5 cm s(-1), with an exponent approximately 0.5 consistent with predictions from the heat transfer theory for simple geometrical objects and typical of laminar boundary layer processes. Measurements of mass transfer across the diffusive boundary layer using O(2) microelectrodes revealed a greater exponent for mass transfer when compared with heat transfer, indicating that heat and mass transfer at the surface of corals are not exactly analogous processes.