Our study investigated the mechanisms sustaining cyanobacteria blooms when CO₂ is depleted in lake surface waters. We found that when lake CO₂ concentrations drop below those of the atmosphere, cyanobacteria switch on carbon concentrating mechanisms (CCMs), allowing them to actively take up bicarbonate. This may provide bloom-forming cyanobacteria with a competitive advantage over other algae. These results provide insight into the timing and duration of blooms in high-nutrient lakes.