On the Great Barrier Reef, summer marine heatwaves are characterised by prolonged, extremely warm sea surface temperatures that have been associated with mass coral bleaching events. Characterising subsurface ocean temperature variability is critical for providing a greater understanding of the impact of temperature extremes on ecosystems at depth. This study explores the relationship between marine heatwaves and the variability of subsurface temperature within the central Great Barrier Reef, using remotely sensed sea surface temperature, measurements from long-term moorings and ocean gliders delivered by the Integrated Marine Observing System, temperature loggers, and the eReefs hydrodynamic model. Here, the East Australian Current flows poleward with a branch entering the lagoon. This onshore branch allows cooler bottom waters to flow onto the shelf through reef passages and remain undetected at the sea surface. During periods of weak or poleward winds, the thermocline rises causing intrusive bottom cooling while heat accumulates over the shallow thermocline causing surface warming. In comparison, extreme wind events including tropical cyclones can cool marine heatwaves, whilst also causing extreme and rapid subsurface warming. The changes in sea surface temperature differ markedly from near-bottom temperature, suggesting heat stress predictions at the surface may not be representative at depth.