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Phytoplankton blooms are increasing in frequency, intensity, and duration in aquatic ecosystems worldwide. In many eutrophic lakes, these high levels of primary productivity correspond to periods of CO₂ depletion in surface waters. Cyanobacteria and other groups of phytoplankton have the ability to actively transport bicarbonate (HCO₃⁻) across their cell membrane when CO₂ concentrations are limiting, possibly giving them a competitive advantage over algae not using carbon concentrating mechanisms (CCMs). To investigate whether CCMs can maintain phytoplankton bloom biomass under CO₂ depletion, we measured the <i>δ</i>¹³C signatures of dissolved inorganic carbon (<i>δ</i>¹³C_DIC) and phytoplankton particulate organic carbon (<i>δ</i>¹³C_phyto) in 16 mesotrophic to hypereutrophic lakes during the ice-free season of 2012. We used mass–balance relationships to determine the dominant inorganic carbon species used by phytoplankton under CO₂ stress. We found a significant positive relationship between phytoplankton biomass and phytoplankton <i>δ</i>¹³C signatures as well as a significant nonlinear negative relationship between water column <i>ρ</i>CO₂ and isotopic composition of phytoplankton, indicating a shift from diffusive uptake to active uptake by phytoplankton of CO₂ or HCO₃⁻ during blooms. Calculated photosynthetic fractionation factors indicated that this shift occurs specifically when surface water CO₂ drops below atmospheric equilibrium. Our results indicate that active HCO₃⁻ uptake via CCMs may be an important mechanism in maintaining phytoplankton blooms when CO₂ is depleted. Further increases in anthropogenic pressure, eutrophication, and cyanobacteria blooms are therefore expected to contribute to increased bicarbonate uptake to sustain primary production.