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Abstract: Understanding the effect of upwelling systems on the carbon cycle requires detailed knowledge of how nutrients and carbon enter and leave these systems. In this article we use recent findings of the JGOFS equatorial Pacific process study and a detailed three-dimensional model to look specifically at the nitrate budget in the equatorial Pacific. Nitrate enters the equatorial upwelling system in the far-western Pacific via the Equatorial Undercurrent. Because the equatorial biota tend to recycle nitrogen much more effectively than they export nitrogen in sinking particles, nitrate stocks build up in the eastern Pacific. A significant fraction of the nitrate entering the upwelling system seems to be lost to denitrification in the anoxic zones off Peru and Central America. Through denitrification, the equatorial upwelling system may function as a regulator of global nitrate stocks and air-sea partitioning of CO₂.