N is a crucial nutrient that limits phytoplankton growth in large ocean areas. The amount of oceanic N is governed by the balance of N₂ fixation and denitrification. Here we incorporate benthic denitrification into an Earth system model with variable particulate stoichiometry. Our model compares better to the observed surface nutrient distributions, marine N₂ fixation, and primary production. Benthic denitrification plays an important role in marine N and C cycling and hence the global climate.