Cilia-­ induced vortical flows are critical for regulating oxygen (O2) and metabolite exchange across coral-­ water in-

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terfaces. While this active ventilation affects the coral tissue microenvironment, its role in thermal stress remains

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poorly understood. Using high-­ speed imaging of cilia beating, particle image velocimetry with O2-

­ sensitive

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nanoparticles, and a mechanistic transport model, we quantified how ciliary dynamics in the reef-­ building coral

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Porites lutea respond to acute warming in darkness. Moderate warming (~35°C) enhanced ciliary activity and ad-

vective transport yet paradoxically thickened the concentration boundary layer with O2-

­ depleted water, exposing

tissues to transient hypoxia. At higher temperatures, ventilation failed to meet rising metabolic demands and

anoxic regions expanded rapidly. Above ~37°C, ciliary coordination collapsed and vortical flows dissipated, shift-

ing transport to a diffusion-­ limited regime accelerating coral mortality. These results identify ciliary beating as a

key regulator of thermal tolerance and early indicator of critical physiological tipping points for reef-­ building cor-

als in a warming, deoxygenating ocean.