- Nitrate is considered the most common non-point pollutant in groundwater. It is often attributed to agricultural management, when excess application of nitrogen fertilizer leaches below the root zone and is eventually transported as nitrate through the unsaturated zone to the water table. A lag time of years to decades between processes occurring in the root zone and their final imprint on groundwater quality prevents proper decision-making on land use and groundwater-resource management. In this study, water flow and solute transport through the deep vadose zone underlying an agricultural field were monitored using a vadose-zone monitoring system (VMS). Data obtained by the VMS over a period of 6 years allowed detailed tracking of water percolation and nitrate migration from the surface through the entire deep vadose zone to the water table at 18 m depth. The temporal variations in the vadose zone sediment water content were used to evaluate the link between rain patterns and water fluxes. A nitrate concentration time series, which varied with time and depth, revealed – in real time – a major pulse of nitrate mass propagating down through the vadose zone from the root zone toward the water table. Analysis of stable nitrate isotopes indicated that manure is the prevalent source of nitrate in the deep vadose zone, and these isotopes were barely affected by natural soil or industrial nitrogen components. Total nitrate mass estimations and simulated pore-water velocity using the analytical solution of the convection–dispersion equation indicated dominance of nitrate vertical transport, and excluded the possibility of lateral nitrate input. Accordingly, prevention of groundwater pollution from surface sources such as agriculture has to include effective and continuous monitoring of the entire vadose zone.