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Ecosystem carbon dioxide (CO2), water vapor, and heat exchanges in alpine wetlands on the Qinghai-Tibetan Plateau are not comprehensively understood. Thus, we studied variability of net ecosystem CO2 exchange (NEE), ecosystem respiration (Re), gross primary production (GPP), evapotranspiration (ET), and heat fluxes over a headwater wetland ecosystem in the Qinghai Lake region. Results showed that the headwater wetland ecosystem was net CO2 absorption on the annual scale, in which monthly NEE, GPP, and Re in two consecutive years varied from -165.16 to 93 g CO2 m(-2 )mo(-1), 6.66 to 384.45 g CO2 m(-2) mo(-1), and 6.9 to 232.02 g CO2 m(-2 )mo(-1), respectively. The monthly ET from June to September was smaller than precipitation; these results reversed in the remaining months. Annual ET was 362.1 mm in 2015 and 324.96 mm in 2016. The net radiation (R-n), sensible heat (H), latent heat (LE), and ground heat (G) fluxes showed similar monthly patterns. Values of monthly average half-hour R-n, H, LE, and G at the daytime showed R-n > LE > H > G, and the time of the monthly half-hour G peak obviously lagged the R-n, H, and LE. Monthly average Bowen ratios were <1 from May to October, but it reversed in the rest of the months.