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The aim of this paper is to apply a new lane separation methodology for the maritime sector emissions attributed to the different vessel types and marine traffic loads in the Mediterranean and the Black Sea defined via the European Marine and Observation Data network (EMODnet), developed in 2016. This methodology is implemented for the first time on the Copernicus Atmospheric Monitoring Service Global Shipping (CAMS-GLOB-SHIP v2.1) nitrogen oxides (NOX) emissions inventory, on the Sentinel-5 Precursor Tropospheric Monitoring Instrument (TROPOMI) nitrogen dioxide (NO2) tropospheric vertical column densities, and on the LOTOS-EUROS (Long Term Ozone Simulation—European Operational Smog) CTM (chemical transport model) simulations. By applying this new EMODnet-based lane separation method to the CAMS-GLOB-SHIP v2.1 emission inventory, we find that cargo and tanker vessels account for approximately 80% of the total emissions in the Mediterranean, followed by fishing, passenger, and other vessel emissions with contributions of 8%, 7%, and 5%, respectively. Tropospheric NO2 vertical column densities sensed by TROPOMI for 2019 and simulated by the LOTOS-EUROS CTM have been successfully attributed to the major vessel activities in the Mediterranean, the mean annual NO2 load of the observations and the simulations reported for the entire maritime EMODnet-reported fleet of the Mediterranean is in satisfactory agreement, 1.26 ± 0.56 × 1015 molecules cm−2 and 0.98 ± 0.41 × 1015 molecules cm−2, respectively. The spatial correlation of the annual maritime NO2 loads of all vessel types between observation and simulation ranges between 0.93 and 0.98. On a seasonal basis, both observations and simulations show a common variability. The wintertime comparisons are in excellent agreement for the highest emitting sector, cargo vessels, with the observations reporting a mean load of 0.98 ± 0.54 and the simulations of 0.81 ± 0.45 × 1015 molecules cm−2 and correlation of 0.88. Similarly, the passenger sector reports 0.45 ± 0.49 and 0.39 ± 0.45 × 1015 molecules cm−2 respectively, with correlation of 0.95. In summertime, the simulations report a higher decrease in modelled tropospheric columns than the observations, however, still resulting in a high correlation between 0.85 and 0.94 for all sectors. These encouraging findings will permit us to proceed with creating a top-down inventory for NOx shipping emissions using S5P/TROPOMI satellite observations and a data assimilation technique based on the LOTOS-EUROS chemical transport model.