Climate extremes intensify global lake eutrophication by increasing the stress resistance of harmful bloom-forming algae.

Lake eutrophication is increasingly shaped by climate extremes, but how short-lived events yield persistent blooms remains unclear. Using global satellite records and laboratory and field experiments, here we show that heatwaves and extreme precipitation drive bloom dynamics beyond gradual warming. In harmful bloom-forming algae (HBFA), heatwaves trigger oxidative stress that rapidly induces intracellular polyphosphate and stabilisomes, dense polyphosphate-rich organelles. As intracellular ballast, stabilisomes drive downward migration, enabling access to sediment-derived phosphorus while avoiding thermal stress; CO2 depletion elevates pH and reinforces a thermo-alkaline cascade amplification effect. Extreme precipitation delivers pulsed phosphorus inputs that are stored as intracellular polyphosphate, creating long-lived phosphorus reserves that prime later heatwaves. When precipitation pulses precede heatwaves, stabilisome formation, vertical migration, and bloom expansion are amplified, even in oligotrophic lakes. Compound climate extremes thus convert episodic disturbances into sustained ecological advantages, challenging nutrient-centric models and redefining bloom-risk prediction and management.