AbstractNewly developed ecosystem model NEMO-Nordic-SCOBI was applied to Skagerrak - Kattegat area to investigate the variability of some indicators of the ecosystem. Also, two sensitivity runs were performed to investigate possible effect of the Baltic Sea Action Plan (BSAP) and a river loads reduction scenario on the Skagerrak - Kattegat area. The performed investigation could be used “to provide a basis to assist with the interpretation of measurement data before the Intermediate Assessments Eutrophication status assessment”. Comparison of simulation results with observations indicates acceptable model performance. Modeled sea surface salinity, temperature and dissolved inorganic phosphate (DIP) are in good agreement with observations. At the same time, the model has a bias in certain areas of the investigated region for dissolved inorganic nitrogen (DIN) and dissolved silicate during the winter season. However, the model in its current state shows good enough results for the performed investigation. Results of the two sensitivity studies show a decrease of sea surface nutrients concentrations during winter period in both regions. In the Skagerrak area the decrease is due to reduction in river nutrient loads in North Sea. In the Kattegat area there is a decrease of dissolved phosphate due to the implementation of BSAP. At the same time, in both scenarios, no significant changes were obtained for near bottom oxygen or surface layer Chl-a.