Marine sediments help us investigate the end of a long period of high ocean productivity that occurred 9 to 3 million years ago. By comparing fossil assemblages of calcifying algae from the Indian and South Atlantic oceans, we found that the dominant, fast-growing species and their ecological prominence determined how and when this period ended in each region, showing that phytoplankton species’ dynamics control large changes in paleoproductivity and carbonate deposition across ocean basins.