Loading of nitrogen (N) from diffuse sources to Danish marine waters was reduced by 41% in the period 1990-2012 by a suite of general measures. However, further reductions in N loading are required if the ambitious quality goals of the EU Water Framework Directive are to be achieved. Measures will be more effective if they are implemented in N loss hot spots or risk areas. Additionally, the highly variable N reduction in groundwater and surface waters needs to be taken into account as this strongly influences the resulting effect of mitigation measures. The objectives of this study were to develop and apply an N risk tool to the entire agricultural land area in Denmark. The purpose of the tool is to identify high risk areas, i.e. areas which contribute disproportionately much to diffuse N losses to the marine recipient, and to suggest cost-effective measures to reduce losses from risk areas. In the N risk mapping part of the tool, we combined a modelled root zone N leaching with a catchment-specific N reduction factor which in combination determines the N load to the marine recipient. N leaching was calculated using detailed information of agricultural management from national databases as well as datasets of percolation and soil parameters as input parameters to an empirical N leaching model. The developed N risk tool showed that the Danish agricultural area is distributed almost evenly between N retention classes (N retention being divided into classes of <40%; 40-60%; 60-80% and >80% N retention). Hot spots for marine N loading are, however, mainly located in catchments with N retention less than 80%. Hot spots for N leaching from the root zone are mainly located in the western part of Jutland, while hot spots for marine N loading are found in all regions and especially in small catchments close to the coast. In a case study for the catchment of the Danish Odense Fjord estuary, we demonstrated how the tool facilitates cost-effective implementation of measures and how measures can be combined to reach a given reduction target for an estuary.