<p>We aimed to evaluate how hydrological condition in temporary wetlands influence CO₂ fluxes and to assess the effect of landscape on the environmental drivers controlling these fluxes. We investigated CO₂ fluxes in Patagonian temporary wetlands during two hydrological phases (dry and aquatic) and three contrasting landscapes (forest, suburban, steppe) to identify the key drivers influencing respiration and gross primary production. We hypothesized that the CO₂ fluxes from wetlands and their drivers are influenced by the hydrological phases and the surrounding landscape. We found that wetlands are net CO₂ sinks during the dry phase (Net Ecosystem Exchange − NEE_dry: -84 ± 16 mmol CO₂ m^− 2d^− 1) and net sources during the aquatic phase (NEE_aquatic: 68 ± 6 mmol CO₂ m^− 2d^− 1). The highest CO₂ emissions originated from bare soil. The wetland landscape did not influence NEE, but respiration and gross primary productivity fluxes were higher in the suburban landscape. The main drivers of NEE were soil temperature, moisture, organic matter content, and vegetation biomass during the dry phase, and dissolved organic carbon and nitrogen concentration during the aquatic phase. Our results show that global change threats in Patagonia, which include warmer and drier climate, increasing livestock pressure, and localized urbanization, will increase CO₂ emissions. Our findings provide insights into CO₂ fluxes from low-disturbance wetlands and can help predict the impacts of global change on CO₂ emissions across this ecologically and economically vital ecosystems.</p>