Ocean acidification induced by atmospheric CO2 may be a major threat to marine ecosystems, particularly to calcareous nannoplankton. We show that, during the Aptian (approximately 120 million years ago) Oceanic Anoxic Event 1a, which resulted from a massive addition of volcanic CO2, the morphological features of calcareous nannofossils traced the biological response to acidified surface waters. We observe the demise of heavily calcified nannoconids and reduced calcite paleofluxes at the beginning of a pre-anoxia calcification crisis. Ephemeral coccolith dwarfism and malformation represent species-specific adjustments to survive lower pH, whereas later, abundance peaks indicate intermittent alkalinity recovery. Deepwater acidification occurred with a delay of 25,000 to 30,000 years. After the dissolution climax, nannoplankton and carbonate recovery developed over approximately 160,000 years under persisting global dysoxia-anoxia.