<p>This study present the first quantification of atmospheric emissions of CO₂, CH₄ and N₂O in reservoirs in Uruguay (Palmar and Bonete). Measurements were conducted in the mouth areas of tributaries and near the dam during two contrasting periods of the year: early fall (April 2022) and late spring (December 2022). The reservoirs exhibited significant spatial and temporal variability in gas emissions. CO₂ was the most abundant gas emitted, followed by CH₄ and N₂O. The latter showed low emissions, with the reservoirs often acting as a sink for this gas. When the reservoirs functioned as a CO₂ sink, CH₄ became the gas with the highest global warming potential (GWP). GHG fluxes correlated with factors associated with eutrophication. Specifically, CO₂ fluxes were negatively correlated with chlorophyll <i>a</i> concentration (<i>p</i> = − 0.602), total nitrogen (<i>p</i> = − 0.627), nitrate + nitrite (<i>p</i> = − 0.594), carbohydrates (<i>p</i> = − 0.656) and temperature (<i>p</i> = − 0.680), CH₄ was correlated with the concentration of chlorophyll <i>a</i> (<i>p</i> = 0.769), phycocyanin (<i>p</i> = 0.870), total phosphorous (<i>p</i> = 0.719), and conductivity (<i>p</i> = 0.583), while N₂O did so with sediment total phosphorous (<i>p</i> = 0.759), sediment total nitrogen (<i>p</i> = 0.584) and nitrate + nitrite concentration (<i>p</i> = − 0.598). Our findings emphasize the critical role of eutrophication and primary productivity in GHGs emissions. In the context of rising global temperatures due to climate change, subtropical reservoirs face the risk of “tropicalization”, with potential environmental consequences. Understanding GHGs emissions in these reservoirs, along with the environmental factors driving them, is essential for effective climate change mitigation.</p> Graphical Abstract <p></p> <p>This graphical abstract provides a visual summary of the main drivers of greenhouse gases (GHGs) emissions in the study subtropical reservoirs. The primary source of GHGs emissions is cultural eutrophication, driven by agricultural activities in the basins and the recent establishment of industries discharging phosphorus (P) and nitrogen (N) into the main river channel. The increased inputs of P and N lead to eutrophication and, consequently, to a rise in autochthonous organic matter (OM), which stimulates GHGs emissions. In the case of CO₂, the reservoirs function as net sinks during the warm months due to high primary production, where photosynthetic activity outweighs respiration. In contrast, as temperatures decrease at the end of summer, primary production declines, respiration becomes the dominant metabolic process, and the reservoirs shift to being significant sources of CO₂. During summer, the reservoirs generate substantial amounts of OM, which, following cellular death, settles into the sediments. Under anaerobic conditions, this OM promotes methanogenic activity, as evidenced by the observed CH₄ emissions. Finally, with respect to N₂O, the reservoirs primarily acted as sinks, likely due to efficient denitrification processes in the sediments that reduce N₂O to N₂. This study contributes to the quantification of GHGs emissions and enhances our understanding of the environmental drivers of GHGs dynamics in subtropical reservoirs.</p>