• The Riganqiao peatland was a net water source with emission (kg m −2 yr −1 ) of average 429.3 ± 51.5 from 2013 to 2017. • Impacts of interannual relative humidity (RH) and net radiation (Rn) on water vapor flux were different in each year. • Net CO 2 ecosystem exchange (NEE) was significantly negative related to water vapor flux, whatever in seasonal or interannual scale. Although carbon flux monitoring has been studied extensively in terrestrial ecosystems around the world, water vapor flux based on eddy covariance has received little attention. As a special type of terrestrial ecosystem, wetlands are transitions between land and water, material and energy, and therefore of great significance in times of global change. In wetlands, water vapor flux has a significant impact on micrometeorological environments, making it the main conduit for water vapor exchange between the wetland and the atmosphere. Using an eddy covariance tower, we measured water vapor flux (H 2 O) over four years at the Riganqiao fen in the Zoige peatlands on the eastern Qinghai‐Tibetan Plateau, China. Diurnal H 2 O peaks occurred around 14:00, and annual mean diurnal rate (mmol m −2 s −1 ) was 0.77 ± 0.02, 1.2 ± 0.02, 0.85 ± 0.02, and 0.93 ± 0.02, respectively over the 4 years. Daily H 2 O flux rate was substantially higher between June and August, with peak values of 8836 g m −2 d −1 on DOY (day of year) 161 in 2013. The Riganqiao peatland was a net water source, with an emission average of 429.3 ± 51.5 (kg m −2 yr −1 ). Hydrological and temperature were crucial to seasonal variation in water vapor fluxes in both growing and non-growing seasons, especially the latent heat flux (LE). However, interannual water vapor flux and relative humidity (RH) were significantly positively correlated to water vapor fluxes in 2016 and 2017 but not in 2013 and 2014. Net CO 2 ecosystem exchange (NEE) was significantly negatively related to water vapor flux at seasonal and interannual scales, suggesting that enhanced transpiration of alpine wetland plants will also promote CO 2 absorption over long time scales. Few previous studies have investigated these patterns based on such an interannual monitoring data with eddy covariance tower on the Qinghai‐Tibetan Plateau. Our results suggest that peatland water vapor flux affects not only the micrometeorological environment, but also NEE in wetland ecosystems over long-time scales.