AbstractWetlands play an important role in biodiversity protection and ecosystem services provision but are susceptible to continuous degradation from the urban environment. In this study, objectives have been made to evaluate the spatial and seasonal (dry and wet periods) variations of diffusive fluxes of methane (CH4) and carbon dioxide (CO2) in water–atmosphere interface and limnological variables (water and sediment) in densely urbanized wetland areas of a tropical reservoir located in the São Paulo metropolitan area. Three sampling stations (S1, S2, and S3) covering areas with different levels of aquatic pollution and land use were evaluated. Nonparametric analysis and one-way analysis of variance indicated the spatial and temporal influence of limnological variability on CH4 and CO2 fluxes. In general, S2 presented higher mean emissions for CH4 (0.31 g m−2 day−1) and CO2 (60.9 g m−2 day−1) compared with the other two stations in both sampling periods, in which maximum mean fluxes in S1 were 0.20 g m−2 day−1 and 18.3 g m−2day−1, whereas in S3 the mean values were <0.09 g m−2 day−1 and 3.5 g m−2 day−1 for CH4 and CO2, respectively. These higher emissions in S2 are related to the proximity to point source discharge of raw sewage from a very urbanized area, as well as lower dilution capacity (water depth=0.4 m). S3 showed lower gases emissions, while S1 presented the intermediate gases flows due to the deepest water column (2.5 m) and higher capacity of pollutant dilution. Thus, we associate higher CH4 and CO2 emissions with the proximity of pollution discharges and lower dilution capacity. The results indicate higher emissions for shallow water, highlight the influence of disorderly occupation in urban areas, and clarify that adequate wastewater treatment is urgent to prevent wetland degradation and to minimize CH4 and CO2 emissions.