Atmospheric emissions from vessels at 38 Pacific and Gulf-Caribbean Mexican ports were determined for nitrogen oxides, sulfur dioxide, particulates, carbon monoxide, non-methane volatile organic compounds, and carbon dioxide. The emissions have been estimated using a bottom-up methodology in the maneuver and hoteling phases, by vessel type, from 2005 to 2020. Maritime traffic in Mexico’s Pacific zone contributes approximately with 60% of the country’s total ship emissions, with the remaining 40% in Gulf-Caribbean ports. The highest atmospheric emissions were found at the Manzanillo and Lázaro Cárdenas ports on the Pacific coast, as well as the Altamira and Veracruz ports on the Gulf-Caribbean coast. The contribution of the atmospheric emissions by vessel type at Pacific ports was Container 67%, Bulk Carrier 32%, Tanker 0.8%, and RoRo 0.4%. For Gulf-Caribbean ports it was Container 76%, Bulk Carrier 19%, Tanker 3%, and RoRo 2%. This study incorporates the International Maritime Organization implementations on reductions of sulfur content in marine fuel, from 4.5% mass by mass from 2005 to 2011, to 3.5% from 2012 to 2019, to 0.5% beginning in 2020. Overall, sulfur dioxide emissions were reduced by 89%.