Investigations on CO2 and CH4 emissions from aquatic systems have increased in the last decades, but most studies focus on high-latitude water bodies, with limited information available for tropical and subtropical zones. Here, we compiled CO2 and CH4 emissions by lentic, lotic, and other types of aquatic ecosystems (e.g., floodplains, estuaries, and mangroves) in different biomes in Brazil. We used a literature search of papers published in the last ~ 30 years to analyze reported emission rates, if they were from the diffusive (DF) and/or ebullitive (EB) pathways, and the most used methods. Most studies were carried out in two biomes (Amazon and Atlantic rainforest). The highest emissions were reported in lentic ecosystems (from 0.05 to 4568 mmol CO2 m-2 day-1, and from 0.19 to 348 mmol CH4 m-2 day-1). The DF pathway was more frequently analyzed, and the floating chamber was the most used measurement method. Our analyses indicated the EB pathway can be significant, especially for CH4 in shallow waters. There were many missing data for either DF or EB so we used studies that measured both and system depth to estimate the missing values and then used total emissions (DF+EB) to run predictive models. For the CO2 emissions, pH, water depth, dissolved oxygen, and water temperature were important predictors, whereas the potential drivers for the CH4 emissions were electrical conductivity and the CO2 emissions. More data are necessary to more clearly characterize the drivers of the emissions of such gases, further understand the dynamics of their emissions, as well as refine emission inventories on both regional and global scales in tropical regions.