New agricultural technologies can reduce the emissions of ammonia associated with e.g. manure spreading. Reduced emissions to the atmosphere have the potential to limit the negative impacts of reactive nitrogen (N_r) on terrestrial ecosystems and human health. But could the new technologies transfer more N_r to the watershed instead and hence lead to increased eutrophication in the aquatic environment? In order to answer questions like this a holistic approach is necessary. Therefore a new management tools is under development at the Danish Center for Energy and Environment (DCE), Aarhus University, where models describing the fate of N_r in the relevant compartments (atmosphere, watershed and aquatic systems) are linked.