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Greenhouse gases increased in concentrations over pre-industrial values by 257% for methane and 145% for carbon dioxide in 2016. Such increased levels are the main climate change drivers and may affect aquatic systems that accumulate and carry carbon to the ocean and the atmosphere. Additionally, these systems are sensitive to environmental changes since their physical, chemical and biological properties respond rapidly to changes. Therefore, this study focus on the greenhouse gases dynamic over an urban eutrophic tropical lagoon. Samplings were performed in the Rodrigo de Freitas Lagoon by covering four periods in 2016 (April, June, October and December). Mean diffusive flux was -1,466.8 mg m(-2) d(-1) of carbon dioxide and 113.7 mg m(-2) d(-1) of methane. Regarding the bubbling, fluxes were 58.28 mg m(-2) d(-1) for methane and negligible for carbon dioxide (mean value of 5.01 mg m(-2) d(-1)). Environmental parameters such as depth, water temperature and sediment particle size were strongly related to the fluxes. In conclusion, the region is a sink of carbon dioxide and a source of methane to the atmosphere. Additionally, the rivers discharge impacts the lagoon by generating a methane hotspot emission region.