Abstract. The Baltic Sea is a highly frequented shipping area with busy shipping lanes close to densely populated regions. Exhaust emissions from ship traffic into the atmosphere do not only enhance 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 were simulated with three regional chemistry transport model (CTM) systems, CMAQ, EMEP/MSC-W and SILAM, with grid resolutions between 4 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 emission dataset but different CTMs are used in their typical set-ups. The performance of these models and the shipping contribution to the results of the individual models were evaluated for sulfur dioxide (SO2), nitrogen dioxide (NO2), ozone (O3) and particulate matter (PM2.5). Model results from the three CTMs for total air pollutant concentrations were compared to observations from rural and urban background stations of the AirBase monitoring network in the coastal areas of the Baltic Sea region. Observed PM2.5 in summer was underestimated strongly by CMAQ and to some extent by EMEP/MSC-W. Observed PM2.5 in winter was underestimated by SILAM. In autumn all models were in better agreement with observed PM2.5. The spatial average of the annual mean O3 in the EMEP/MSC-W simulation was ca. 20 % 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. EMEP/MSC-W, with the coarsest grid, predicted weaker ozone depletion through NO emissions in the proximity of the main shipping routes than the other two models. The average contribution of ships to PM2.5 levels in coastal land areas is in the range of 3.1 %–5.7 % 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. Differences in the ship-related elemental carbon (EC) among the CTMs can be explained by differences in the meteorological conditions, atmospheric transport processes and the applied wet-scavenging parameterizations. Overall, results from the present study show the sensitivity of the ship contribution to combined uncertainties in 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.