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Abstract Lake heatwaves (extreme hot water events) can substantially disrupt aquatic ecosystems. Although surface heatwaves are well studied, their vertical structures within lakes remain largely unexplored. Here we analyse the characteristics of subsurface lake heatwaves (extreme hot events occurring below the surface) using a spatiotemporal modelling framework. Our findings reveal that subsurface heatwaves are frequent, often longer lasting but less intense than surface events. Deep-water heatwaves (bottom heatwaves) have increased in frequency (7.2 days decade⁻¹), duration (2.1 days decade⁻¹) and intensity (0.2 °C days decade⁻¹) over the past 40 years. Moreover, vertically compounding heatwaves, where extreme heat occurs simultaneously at the surface and bottom, have risen by 3.3 days decade⁻¹. By the end of the century, changes in heatwave patterns, particularly under high emissions, are projected to intensify. These findings highlight the need for subsurface monitoring to fully understand and predict the ecological impacts of lake heatwaves.