Abstract. Emission factors of SO₂, NO_x and size-distributed particle numbers were measured for approximately 300 different ships in the Gulf of Finland and Neva Bay area during two campaigns in August/September 2011 and June/July 2012. The measurements were carried out from a harbor vessel and from an Mi-8 helicopter downwind of passing ships. Other measurements were carried out from shore sites near the island of Kronstadt and along the Neva River in the urban area of Saint Petersburg. Most ships were running at reduced speed (10 kn), i.e., not at their optimal load. Vessels for domestic and international shipping were monitored. It was seen that the distribution of the SO₂ emission factors is bi-modal, with averages of 4.6 and 18.2 g_SO2 kg_fuel^-1 for the lower and the higher mode, respectively. The emission factors show compliance with the 1% fuel sulfur content Sulfur Emission Control Areas (SECA) limit for 90% of the vessels in 2011 and 97% in 2012. The distribution of the NO_x emission factor is mono-modal, with an average of 58 g_NOx kg_fuel^-1. The corresponding emission related to the generated power yields an average of 12.1 g_NOx kWh⁻¹. The distribution of the emission factors for particulate number shows that nearly 90% of all particles in the 5.6 nm to 10 μm size range were below 70 nm in diameter. The distribution of the corresponding emission factors for the mass indicates two separated main modes, one for particles between 30 and 300 nm and the other for above 2 μm. The average particle emission factors were found to be in the range from 0.7 to 2.7 × 10¹⁶ particles kg_fuel^-1 and 0.2 to 3.4 g_PM kg_fuel^-1, respectively. The NO_x and particulate emissions are comparable with other studies. The measured emission factors were compared, for individual ships, to modeled ones using the Ship Traffic Emission Assessment Model (STEAM) of the Finnish Meteorological Institute. A reasonably good agreement for gaseous sulfur and nitrogen emissions can be seen for ships in international traffic, but significant deviations are found for inland vessels. Regarding particulate mass, the values of the modeled data are about 2–3 times higher than the measured results, which probably reflects the assumptions made in the modeled fuel sulfur content. The sulfur contents in the fuel retrieved from the measurements were lower than the previously used assumptions by the City of Saint Petersburg when carrying out atmospheric modeling, and using these measurements it was possible to better assess the impact of shipping on air quality.