AbstractThe Baltic Sea is highly frequented shipping area with busy shipping lanes close to densely populated regions. Exhaust emissions from ship traffic into the atmosphere are not only enhancing air pollution, they also affect the Baltic Sea environment through acidification and eutrophication of marine waters and surrounding terrestrial ecosystems. As part of the European BONUS project SHEBA (Sustainable Shipping and Environment of the Baltic Sea Region), the transport, chemical transformation and fate of atmospheric pollutants in the Baltic Sea region was simulated with three regional chemistry transport models (CTM) systems, CMAQ, EMEP/MSC-W and SILAM with grid resolutions between 4 km and 11 km. The main goal was to quantify the effect that shipping emissions have on the regional air quality in the Baltic Sea region when the same shipping emissions dataset but different CTMs in their typical setups are used. The performance of these models and the shipping contribution to the results of the individual models was evaluated for sulphur dioxide (SO2), nitrogen dioxide (NO2) and ozone (O3) and particulate matter (PM2.5). Model results from the three CTMs were compared to observations from rural and urban background stations of the AirBase monitoring network in the coastal areas of the Baltic Sea region. The performance of the three CTM systems to predict pollutant concentrations is similar. However, observed PM2.5 in summer was underestimated strongly by CMAQ and to some extent by EMEP/MSC-W. The spatial average of annual mean O3 in the EMEP/MSC-W simulation is 15–25 % higher compared to the other two simulations, which is mainly the consequence of using a different set of boundary conditions for the European model domain. There are significant differences in the calculated ship contributions to the levels of air pollutants among the three models. SILAM predicted a much weaker ozone depletion through NO emissions in the proximity of the main shipping routes than the other two models. In the entire Baltic Sea region the average contribution of ships to PM2.5 levels is in the range of 4.3–6.5 % for the three CTMs. Differences in ship-related PM2.5 between the models are mainly attributed to differences in the schemes for inorganic aerosol formation. Inspection of the ship-related elemental carbon (EC) revealed that assumptions about the vertical ship emission profile can affect the dispersion and abundance of ship-related pollutants in the near-ground atmosphere. The models are in agreement regarding the ship-related deposition of oxidised nitrogen, reporting a ship contribution in the range of 21–23 ktN y−1 as atmospheric input to the Baltic Sea. Results from the present study show the sensitivity of the ship contribution to combined uncertainties of boundary conditions, meteorological data and aerosol formation and deposition schemes. This is an important step towards a more reliable evaluation of policy options regarding emission regulations for ship traffic and the planned introduction of a nitrogen emission control area (NECA) in the Baltic Sea and the North Sea in 2021.