Abstract. The North Sea and the Baltic Sea still experience eutrophication and deoxygenation in spite of large international efforts to mitigate such environmental problems. Due to the highly different oceanographic frameworks of the two seas, modelling efforts so far mainly focused either on one or the other Sea making it difficult to study inter-basin exchange of mass and energy. Here, we present an ocean model (NEMO-Nordic) coupled to the Swedish Coastal and Ocean Biogeochemical model (SCOBI), which covers the North Sea, the Skagerrak-Kattegat transition zone and the Baltic Sea. We address its validity to further investigate biogeochemical changes in the North Sea-Baltic Sea system. The model reproduces the long-term temporal trends, the temporal variability, the yearly averages and the general spatial distribution of all assessed biogeochemical parameters. It is particularly suitable to be used in future multi-stressor studies such as to evaluate combined climate and nutrient forcing scenarios. In particular, the model performance is best for oxygen and phosphate concentrations. However, important seasonal and spatial differences for chlorophyll-a and nitrate are seen between model results and observations in coastal areas of the southeastern North Sea, the Skagerrak-Kattegat transition zone, the Gulf of Riga, the Gulf of Finland and the Gulf of Bothnia. These are partially linked to different local processes and biogeochemical forcing that lead to a general overestimation of nitrate. The validation of our model results for individual areas are in agreement with policy management assessment areas, which gives an added value to better contribute to international programs aiming to reduce eutrophication in the Baltic Sea-North Sea system.