We present a top-down ship NOx emission inventory for the Baltic Sea, the North Sea, the Bay of Biscay and the Mediterranean Sea based on satellite-observed tropospheric NO2 columns of the Ozone Monitoring Instrument (OMI) for 2005–2006. We improved the representation of ship emissions in the GEOS-Chem chemistry transport model, and compared simulated NO2 columns to consistent satellite observations. Relative differences between simulated and observed NO2 columns have been used to constrain ship emissions in four European seas (the Baltic Sea, the North Sea, the Bay of Biscay and the Mediterranean Sea) using a mass-balance approach, and accounting for non-linear sensitivities to changing emissions in both model and satellite retrieval. These constraints are applied to 39 % of total top-down European ship NOx emissions, which amount to 0.96 Tg N for 2005, and 1.0 Tg N for 2006 (11–15% lower than the bottom-up EMEP ship emission inventory). Our results indicate that EMEP emissions in the Mediterranean Sea are too high (by 60%) and misplaced by up to 150 km, which can have important consequences for local air quality simulations. In the North Sea ship track, our top-down emissions amount to 0.05 Tg N for 2005 (35% lower than EMEP). Increased top-down emissions were found for the Baltic Sea and the Bay of Biscay ship tracks, with totals in these tracks of 0.05 Tg N (131% higher than EMEP) and 0.08 Tg N for 2005 (128% higher than EMEP), respectively. Our study explicitly accounts for the (non-linear) sensitivity of satellite retrievals to changes in the a priori NO2 profiles, as satellite observations are never fully independent of model information (i.e. assumptions on vertical NO2 profiles). Our study provides for the first time a space-based, top-down ship NOx emission inventory, and can serve as a framework for future studies to constrain ship emissions using satellite NO2 observations in other seas.