We investigated the combined effect of ocean acidification and warming on the dynamics of the phytoplankton fall boom in the Lower St. Lawrence Estuary, Canada. Twelve 2600 L mesocosms were used to cover a wide range of pH and two temperatures. We found that warming, rather than acidification, is more likely to alter the autumnal bloom in this estuary in the decades to come by stimulating the development and senescence of diatoms, and promoting picocyanobacteria proliferation.