The fate of anthropogenic reactive nitrogen (N) is often described as a cascade of different nitrogen forms and effects throughout the environment. In order to describe the fate in detail, a holistic approach covering the flow between the main environmental compartments is needed. Therefore a new management tools has been setup for an area in Denmark. A holistic approach is attempted by linking models for the main compartments (atmosphere, watershed and aquatic) and including a common emission scenario. The scenario describes a new technique for reducing ammonia emissions and at the same time increase N availability for crops using acidification of liquid manure and use of air cleaners in pig and poultry houses. Here the first results from a pilot study in Northern Jutland, Denmark, will be presented.