Global food production depends on phosphorus. Phosphorus is broadly applied as fertilizer, but excess phosphorus contributes to eutrophication of surface water bodies and coastal ecosystems1. Here we present an analysis of phosphorus fluxes in three large river basins, including published data on fertilizer, harvested crops, sewage, food waste and river fluxes2, 3, 4. Our analyses reveal that the magnitude of phosphorus accumulation has varied greatly over the past 30–70 years in mixed agricultural–urban landscapes of the Thames Basin, UK, the Yangtze Basin, China, and the rural Maumee Basin, USA. Fluxes of phosphorus in fertilizer, harvested crops, food waste and sewage dominate over the river fluxes. Since the late 1990s, net exports from the Thames and Maumee Basins have exceeded inputs, suggesting net mobilization of the phosphorus pool accumulated in earlier decades. In contrast, the Yangtze Basin has consistently accumulated phosphorus since 1980. Infrastructure modifications such as sewage treatment and dams may explain more recent declines in total phosphorus fluxes from the Thames and Yangtze Rivers3, 4. We conclude that human-dominated river basins may undergo a prolonged but finite accumulation phase when phosphorus inputs exceed agricultural demand, and this accumulated phosphorus may continue to mobilize long after inputs decline.