Thermal stratification and mixing play important roles in the physicochemical composition of lakes and affect the geochemical cycle. However, the regulation of lake carbon exchange at the water-air interface by seasonal thermal structures remains unclear, especially for alpine saline lake on the Qinghai-Tibet Plateau (QTP). Based on continuous field sampling, carbon dioxide flux (FCO2) at the water-air interface in Qinghai Lake during the ice-free period was quantitatively analyzed by thin boundary layer model, as well as the driving factors of the change in FCO2 at the water-air interface. The findings revealed that the FCO2 was −22.16 ± 11.73 mmol m−2d−1 during the stratification period, and − 45.32 ± 29.67 mmol m−2d−1 during the mixing period. We found that thermal stratification limits the matter-energy exchange between the upper and bottom water columns, and carbonate precipitation results in a higher FCO2 than during mixing stage. However, the mixing process reduces the limiting effect of thermal stratification. During the carbonate process, water with higher salinity and pH at the bottom of the water column enters the upper part of the water column, reducing the partial pressure of carbon dioxide (pCO2) in the water column and causing the absorption of CO2 by the lake. Thermal stratification affects the vertical material-energy exchange and atmospheric CO2 uptake of lake. The present study further explains the possible underlying regulation of CO2 uptake in saline lake on the QTP involving the varied thermal structure.
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