This paper presents a spatially explicit model for simulating the fate of nitrogen (N) in soil and groundwater and nitrous oxide (N 2O) production in groundwater with a 1 km resolution at the European scale. The results show large heterogeneity of nitrate outflow from groundwater to surface water and production of N 2O. This heterogeneity is the result of variability in agricultural and hydrological systems. Large parts of Europe have no groundwater aquifers and short travel times from soil to surface water. In these regions no groundwater denitrification and N 2O production is expected. Predicted N leaching (16% of the N inputs) and N 2O emissions (0.014% of N leaching) are much less than the IPCC default leaching rate and combined emission factor for groundwater and riparian zones, respectively. © 2012 Elsevier Ltd. All rights reserved.