Budget calculations show that bioavailability of dissolved organic nitrogen (DON) is a key factor in management of eutrophication in open marine areas as it governs the importance of local loadings versus nitrogen received from adjacent seas and hence if eutrophication is a local or regional problem. Nitrogen is the limiting nutrient in the Belt Sea and the Kattegat. At the same time the area is heavily affected by eutrophication. Hence, a number of abatement measures have been implanted in Denmark, Sweden and Germany in order to reduce the anthropogenic nitrogen loadings. In this context it is essential to know how much of the nitrogen comes from local sources and how much is imported for the adjacent seas. We have therefore made nitrogen budgets for both total nitrogen and bioavailable nitrogen covering the area. Bioavailable nitrogen consists of inorganic N, particulate organic N and the bioavailable fraction of DON. Since DON constitutes by far the largest pool of nitrogen, assessment of the bioavailability of DON becomes the most important parameter in the budget. Hence bioavailability of DON also becomes a key issue for management of coastal areas, as it determinates to what extent eutrophication can be managed by local measures or is a more regional problem. The budgets show that direct local loadings with freshwater and atmospheric deposition accounts for 26% of the total TN input but 43% of the bioavailable input for the period 2000–2009. In the 1980s the direct local loadings of bioavailable nitrogen is estimated to be 53%.