Mexico City is a large city, populated by 8.8 million inhabitants. This population density, combined with poor wastewater management, results in aquatic ecosystems receiving a large volume of wastewater which may promote methane (CH4) emission. We measured water quality and CH4 emission from 11 aquatic ecosystems in Mexico City during 1 year, including reservoirs, rivers, lakes, canals and chinampas (system of floating garden on shallow lakes). The total CH4 emission from aquatic ecosystems was estimated as 3679 Mg CH4 year-1, which represents 3.5 % of the annual CH4 emission of Mexico City. The main contributors are chinampas (33 %), followed by lakes (27 %), reservoirs (19 %), rivers (12 %) and canals (9 %). Water quality indicators were positively correlated with CH4 emission, therefore a decrease in untreated wastewater discharge may result in a significant reduction of the greenhouse gas footprint of Mexico City, after a transitional period during which the organic content of the sediment would be degraded.