Reaching the EU quality standard for nitrate (50 mg NO3/L) in all groundwater bodies is a challenge in the Federal State of North Rhine-Westfalia (Germany). In the research project GROWA+ NRW 2021 initiated by the Federal States’ Ministry for Environment, Agriculture, Nature and Consumer Protection, amongst other aspects, a model-based analysis of agricultural nitrogen inputs into groundwater and nitrate concentration in the leachate was carried out. For this purpose, the water balance model mGROWA, the agro-economic model RAUMIS, and the reactive N transport model DENUZ were coupled and applied consistently across the whole territory of North Rhine-Westfalia with a spatial resolution of 100 m × 100 m. Besides agricultural N emissions, N emissions from small sewage plants, urban systems, and NOx deposition were also included in the model analysis. The comparisons of the modelled nitrate concentrations in the leachate of different land use influences with observed nitrate concentrations in groundwater were shown to have a good correspondence with regard to the concentration levels across all regions and different land-uses in North Rhine-Westphalia. On the level of ground water bodies (according to EU ground water directive) N emissions exclusively from agriculture led to failure of the good chemical state. This result will support the selection and the adequate dimensioning of regionally adapted agricultural N reduction measures.