Over geological time, photosynthetic carbon fixation in the oceans has exceeded respiratory oxidation of organic carbon. The imbalance between the two processes has resulted in the simultaneous accumulation of oxygen in, and drawdown of carbon dioxide from, the Earth's atmosphere, and the burial of organic carbon in marine sediments1–3. It is generally assumed that these processes are limited by the availability of phosphorus4,5, which is supplied by continental weathering and fluvial discharge5–7. Over the past two million years, decreases in atmospheric carbon dioxide concentrations during glacial periods correlate with increases in the export of organic carbon from surface waters to the marine sediments8–11, but variations in phosphorus fluxes appear to have been too small to account for these changes12,13. Consequently, it has been assumed that total oceanic primary productivity remained relatively constant during glacial-to-interglacial transitions, although the fraction of this productivity exported to the sediments somehow increased during glacial periods12,14. Here I present an analysis of the evolution of biogeochemical cycles which suggests that fixed nitrogen, not phosphorus, limits primary productivity on geological timescales. Small variations in the ratio of nitrogen fixation to denitrification can significantly change atmospheric carbon dioxide concentrations on glacial-to-interglacial timescales. The ratio of these two processes appears to be determined by the oxidation state of the ocean and the supply of trace elements, especially iron.