Ocean acidification, the change in seawater carbonate chemistry due to the uptake of anthropogenic CO₂, affects the physiology of marine organisms in multiple ways¹. Diverse competitive and trophic interactions transform the metabolic responses to changes in community composition, seasonal succession and potentially geographical distribution of species. The health of ocean ecosystems depends on whether basic biotic functions are maintained, ecosystem engineers and keystone species are retained, and the spread of nuisance species is avoided². Here, we show in a field experiment that the toxic microalga Vicicitus globosus has a selective advantage under ocean acidification, increasing its abundance in natural plankton communities at CO₂ levels higher than 600 µatm and developing blooms above 800 µatm CO₂. The mass development of V. globosus has had a dramatic impact on the plankton community, preventing the development of the micro- and mesozooplankton communities, thereby disrupting trophic transfer of primary produced organic matter. This has prolonged the residence of particulate matter in the water column and caused a strong decline in export flux. Considering its wide geographical distribution and confirmed role in fish kills³, the proliferation of V. globosus under the IPCC⁴ CO₂ emission representative concentration pathway (RCP4.5 to RCP8.5) scenarios may pose an emergent threat to coastal communities, aquaculture and fisheries.