Nitrate in groundwater is increasing in many aquifers worldwide due to excessive use of fertilizers. However, the behavior of N-based fertilizer as it leaches through thick vadose zones is still poorly understood, and the long-term effects on groundwater quality in such settings may yet to be fully realized. In this study, deep soil cores were taken below experimental plots where N-fertilizer was applied for nearly 20 years under wheat-maize double cropping in the North China Plain (NCP). N-fertilizer application rates of zero, 400, and 600 kg N ha−1 yr−1 were applied to different plots. Water and N balances were quantified to estimate the leaching rate of NO3−-N below the root zone, and NO3−-N loss via denitrification. Transport pathways of nitrate in the vadose zone were identified using stable isotopes of water (δ18O-H2O & δ2H-H2O) and nitrate (δ18O-NO3− & δ15N-NO3−) from the sampled pore-water and groundwater. The average N transport velocity through the vadose zone ranged from 38 to 41 cm yr−1 and was relatively constant regardless of fertilizer application rate. The transport rates are significantly lower than the long-term rate of groundwater level decline (100 cm yr−1), meaning it is unlikely much of the leachate from chemical N-fertilizers (abundantly applied throughout the region since the 1970s) has entered groundwater via matrix flow. Nitrate isotopes appear to indicate that manure and septic waste (not chemical N-fertilizer) are the major sources of nitrate in groundwater to date. However, stable isotopes show that increased nitrate concentrations in groundwater may also result due to preferential flow in sand layers and/or lateral flow from headwater areas. Denitrification (particularly in the upper 4 m depth of soil) appears to have limited the flux of fertilizer-derived nitrate to some degree. However, the large N stock and generally weak denitrification potential in the deep unsaturated zone, pose a major threat to future groundwater quality. The results have major implications for groundwater quality management in the future.