Physical and biological factors have been proposed to account for the long-term development of marine biodiversity through the Phanerozoic Eon. Nutrient availability and primary productivity have, however, received less attention. We demonstrate that the diversification of the major marine faunas during the Phanerozoic was coupled to nutrient runoff from land and the diversification of phosphorus-rich plankton. Nutrient input to the oceans increased dramatically during the Meso-Cenozoic in response to widespread orogeny and peaked repeatedly following the eruption and weathering of phosphorus-rich continental Large Igneous Provinces. Widespread orogeny, forestation, and nutrient runoff during the Permo-Carboniferous was transitional to the Mesozoic and continued during the later Mesozoic and Cenozoic eras with the further tectonism and the spread of angiosperms, modern representatives of which tend to be more nutrient-rich. Early-to-middle Paleozoic diversity was, in contrast, limited by nutrient-poor plankton resulting from less frequent tectonism and poorly-developed terrestrial floras. Our results suggest that biodiversity on geologic time scales is unbounded, provided sufficient nutrients and nutrient-rich plankton are available on optimal timescales.