Urban areas are increasingly adopting nature-based solutions to enhance biodiversity and human well-being. The naturalization of artificial urban ponds (AUPs) is one such strategy, offering ecological benefits. However, concerns remain about its potential impact on greenhouse gas (GHG) emissions. In this study, we measured the partial pressures of CO₂ (ρCO₂), CH₄ (ρCH₄), and N₂O (ρN₂O) in 41 AUPs (28 naturalized, 13 non-naturalized) across winter and summer to assess: (i) the impact of naturalization, (ii) seasonal variations, and (iii) key environmental drivers of GHG emissions. Our results indicate that naturalization increased ρCH₄ but reduced ρN₂O, with no significant effect on ρCO₂. The primary factors driving these patterns included naturalization—particularly through effects on primary production—seasonality, with temperature playing a key role, and groundwater legacy. Importantly, the net global warming potential, expressed as CO₂ equivalents, did not significantly differ between naturalized and non-naturalized ponds. To further investigate the role of vegetation in modulating GHG fluxes, we compared fluxes from open water, and areas dominated by floating, emergent, and submerged vegetation in two naturalized AUPs across diurnal cycles in winter and summer. CH₄ emissions were highest from submerged vegetation zones, followed by emergent vegetation areas. While emergent and floating vegetation absorbed CO₂ during the day, they emitted it at night. N₂O was consistently emitted from open water, floating, and submerged vegetation zones, but unexpectedly, emergent vegetation areas absorbed N₂O throughout both day and night. Overall, our findings suggest that naturalizing AUPs can enhance urban resilience without substantially increasing GHG emissions. Moreover, promoting floating vegetation over submerged and emergent vegetation could help mitigate GHG emissions in naturalized AUPs.