National terrestrial nitrogen budgets for many developed countries have been calculated as part of the management of impacts of N on the environment, but these rarely represent the subsurface explicitly. Using estimates of vadose zone travel time and agricultural nitrate loading, we quantify, for the first time, the total mass of nitrate contained in the vadose zone of aquifers in England and Wales. This mass peaked in 2008 at 1400 kt N (800 to >1700 kt N from sensitivity analyses), which is approximately 2.5 to 6 times greater than saturated zone estimates for this period and indicates that the subsurface is an important store of reactive nitrogen. About 70% of the nitrate mass is estimated to be in the Chalk, with the remainder split between the Permo-Triassic sandstones, the Jurassic Oolitic limestones and minor aquifers. Current controls on fertilizer application mean that the vadose zone is now a nitrate source, and in 2015 we estimate the net flux from the unsaturated zone to groundwater to be 72 kt N/a. The mass of nitrate in the vadose zone should be included in future terrestrial nitrogen budgets at national and global scales to improve ecosystem management. British Geological Survey © NERC 2015. Hydrological Processes © 2015 John Wiley & Sons, Ltd.