Nitrate (N) leaching from intensively managed cropping systems is of environmental concern and it varies at local scale. To evaluate the performance of agricultural practices at this scale, there is a need to develop comprehensive assessments of N leaching and the N leaching reduction potential of mitigation measures. A model-based analysis was performed to (i) estimate N leaching from Danish cropping systems, representing 20 crop rotations, 3 soil types, 2 climates and 3–4 levels of manure (slurry)-to-fertilizer ratios, but with same available N (according to regulatory N fertilization norms), and (ii) appraise mitigation potential of on-farm measures (i.e. catch crops, early sowing of winter cereals) to reduce N leaching. The analysis was performed using a process-based agro-environmental model (Daisy). Simulated average N leaching over 24 years ranged from 16 to 85 kg N/ha/y for different crop rotations. Rotations with a higher proportion of spring crops were more prone to leaching than rotations having a higher proportion of winter cereals and semi-perennial grass-clover leys. N leaching decreased with increasing soil clay content under all conditions. The effect of two climates (different regions, mainly differing in precipitation) on N leaching was generally similar, with slight variation across rotations. Supplying a part of the available N as manure-N resulted in similar N leaching as mineral fertilizer N alone during the simulation period. Among the mitigation measures, both undersown and autumn sown catch crops were effective. Effectiveness of measures also depended on their place and frequency of occurrence in a rotation. Adopting catch crops during the most leaching-prone years and with higher frequency were effective choices. This analysis provided essential data-driven knowledge on N leaching risk, and potential of leaching reduction options. These results can serve as a supplementary guiding-tool for farmers to plan management practices, and for legislators to design farm-specific regulatory measures.