<p>Heatwaves are intensifying globally, reshaping the carbon and nitrogen cycles of shallow lakes. In arid regions, concurrent salinization driven by climate change and water abstraction further modifies greenhouse gas (GHG) emissions. We investigated how short-term heatwaves and warming influence GHG fluxes in shallow lakes differing in salinity and macrophyte coverage, using outdoor mesocosms in two contrasting climatic zones of Türkiye: Mersin (hot Mediterranean) and Ankara (cold semiarid). The 2022 heatwave 22 experiment (Aug.–Nov.) used 32 mesocosms (16 per site) at two salinities (4 and 40) exposed to a simulated 15-d heatwave targeting +5 °C, with twice-weekly GHG sampling. In 2023, a second 30-d warming experiment in Mersin site targeting +4.5-°C difference assessed longer-term effects with daily measurements. Seasonal temperature variation and salinity with associated ecosystem characteristics (like, macrophyte presence) emerged as the main drivers of GHG fluxes, while short-term heating had weak and context-dependent impacts. Methane (CH₄) emissions were consistently higher at Mersin than Ankara but generally low and declined with seasonal cooling, showing no clear heatwave response. Nitrous oxide (N₂O) emissions were near zero in the low salinity, macrophyte-dominated mesocosms and remained unaffected throughout the experiment. In contrast, the high salinity mesocosms showed greater variability, albeit with no clear heatwave response. Carbon dioxide (CO₂) emissions show a weak heatwave response only after the 15-d heatwave period, suggesting a lagged response. During the longer warming experiment, however, high-salinity, macrophyte-free mesocosms shifted from net CO₂ uptake to emission, after 30 d of warming. Overall, our findings show that salinity and macrophyte coverage, rather than short-term temperature extremes, may primarily regulate GHG emissions in shallow lakes, while prolonged warming may alter carbon cycling in high-salinity, macrophyte-free lake ecosystems.</p>