Description: The Baltic Sea is a severely eutrophicated sea-area where intense shipping as an additional nutrient source is a potential contributor to changes in the ecosystem. The impact of the two most important shipborne nutrients, nitrogen and phosphorus, on the overall nutrient-phytoplankton-oxygen dynamics in the Baltic Sea was determined by using the coupled physical and biogeochemical model system General Estuarine Transport Model–Ecological Regional Ocean Model (GETM-ERGOM) in a cascade with the Ship Traffic Emission Assessment Model (STEAM) and the Community Multiscale Air Quality (CMAQ) model. We compared two nutrient scenarios in the Baltic Sea: with (SHIP) and without nutrient input from ships (NOSHIP). The model uses the combined nutrient input from shipping-related waste streams and atmospheric depositions originating from the ship emission and calculates the effect of excess nutrients on the overall biogeochemical cycle, primary production, detritus formation and nutrient flows. The shipping contribution is about 0.3% of the total phosphorus and 1.25–3.3% of the total nitrogen input to the Baltic Sea, but their impact to the different biogeochemical variables is up to 10%. Excess nitrogen entering the N-limited system of the Baltic Sea slightly alters certain pathways: cyanobacteria growth is compromised due to extra nitrogen available for other functional groups while the biomass of diatoms and especially flagellates increases due to the excess of the limiting nutrient. In terms of the Baltic Sea ecosystem functioning, continuous input of ship-borne nitrogen is compensated by steady decrease of nitrogen fixation and increase of denitrification, which results in stationary level of total nitrogen content in the water. Ship-borne phosphorus input results in a decrease of phosphate content in the water and increase of phosphorus binding to sediments. Oxygen content in the water decreases, but reaches stationary state eventually.