Nitrate–nitrogen is a groundwater contaminant worldwide that originates commonly from agricultural fertilization. In this work, we built a computer model which follows the fate of nitrogen from land surface to deep (~100 m) and distant (~km) groundwater wells. The model succeeded estimating total groundwater nitrate, yet failed to point-estimate contaminated wells, extra assumptions fixed it. This enabled prediction of future groundwater–nitrate which revealed the need to reduce fertilization.