AbstractInland waters play an important role in the global carbon cycle and are potential hotspots of greenhouse gas (GHG) production and emission. However, considerable uncertainty exists in GHG estimations from lakes on the Tibetan Plateau due, in part, to the lack of direct in situ observations and key predictor analyses. Considering that salinity is an important factor regulating lake GHGs, diffusive methane flux (FCH₄) and carbon dioxide flux (FCO₂) and concentrations of dissolved CH₄ (dCH₄) and CO₂ (dCO₂) were measured in 16 freshwater and brackish Tibetan lakes in Shigatse. The results demonstrated that FCH₄ at the water–air interface in freshwater lakes (45.14 ± 58.86 μmol·m⁻²·s⁻¹) was 15 times higher than that in brackish lakes (2.92 ± 3.85 μmol·m⁻²·s⁻¹). There was a significant decrease in FCH₄ from the littoral zone to the pelagic area in these lakes. The FCO₂ in freshwater lakes (−0.18 ± 0.39 μmol·m⁻²·s⁻¹) was significantly lower than that in brackish lakes (0.38 ± 0.22 μmol·m⁻²·s⁻¹). Therefore, freshwater lakes were regarded as CO₂ sinks, while brackish lakes were regarded as CO₂ sources. According to the comprehensive CO₂ equivalent diffusive fluxes (FCO₂eq, 0.66 ± 0.97 μmol·m⁻²·s⁻¹), the 16 lakes were a carbon source to the atmosphere during the sampling period. FCO₂ enhancement could be compensated by the decrease in FCH₄ at the water–air interface as a result of salinity gradients across lakes. Under the scenarios of climate warming and drying in southern Tibet from 2020 to 2035, lake FCO₂eq tended to decrease in this area.