A key aspect of protecting aquatic ecosystems from agricultural nitrogen (N) is to locate (i) farmlands where nitrate leaches from the bottom of the root zone and (ii) denitrifying zones in the aquifers where nitrate is removed before entering the surface water (N-retention). N-retention affects the choice of field mitigation measures to reduce delivered N to surface water. Farmland parcels associated with high N-retention gives the lowest impact of the targeted field measures and vice versa. In Denmark, a targeted N-regulation approach is currently implemented on small catchment scale (approx. 15 km²). Although this regulatory scale is much more detailed than what has been used previously, it is still so large that regulation for most individual fields will be either over- or under-regulated due to large spatial variation in the N-retention. The potential cost reduction for farmers is of up to 20–30% from detailed retention mapping at the field scale compared to the current small catchment scale. In this study, we present a mapping framework (N-Map) for differentiating farmland according to their N-retention, which can be used for improving the effectiveness of targeted N-regulation. The framework currently only includes N-retention in the groundwater. The framework benefits from the incorporation of innovative geophysics in hydrogeological and geochemical mapping and modelling. To capture and describe relevant uncertainties a large number of equally probable realizations are created through Multiple Point Statistical (MPS) methods. This allows relevant descriptions of uncertainties of parts of the model structure and includes other relevant uncertainty measures that affects the obtained N-retention. The output is data-driven high-resolution groundwater N-retention maps, to be used by the individual farmers to manage their cropping systems due to the given regulatory boundary conditions. The detailed mapping allows farmers to use this information in the farm planning in order to optimize the use of field measures to reduce delivered agricultural N to the surface water and thereby lower the costs of the field measures. From farmer interviews, however, it is clear that not all farms will have an economic gain from the detailed mapping as the mapping costs will exceed the potential economic gains for the farmers. The costs of N-Map is here estimated to 5–7 €/ha/year plus implementation costs at the farm. At the society level, the N-retention maps allow authorities to point out opportunities for a more targeted implementation of field measures to efficiently reduce the delivered N-load to surface waters.