Upwelling of nutrient-rich deep waters to the surface make eastern boundary upwelling systems hot spots of marine productivity. This leads to subsurface oxygen depletion and the transformation of bioavailable nitrogen into inert N₂. Here we quantify nitrogen loss processes following a simulated deep water upwelling. Denitrification was the dominant process, and budget calculations suggest that a significant portion of nitrogen that could be exported to depth is already lost in the surface ocean.