Summary: Climate change and human activities have intensified variations of water table depth (WTD) in wetlands around the world, which may strongly affect greenhouse gas emissions. Here, we analyzed how emissions of CO2, CH4, and N2O from the Zoige wetland on the Qinghai-Tibetan Plateau (QTP) vary with the WTD. Our data indicate that the wetland shows net positive global warming potential (11.72 tCO2-e ha−1 yr−1), and its emissions of greenhouse gases are driven primarily by WTD. Our analysis suggests that an optimal WTD exists, which at our study site was approximately 18 cm, for mitigating increases in global warming potential from the wetland. Our study provides insights into how climate change and human acitivies affect greenhouse gas emissions from alpine wetlands, and they suggest that water table management may be effective at mitigating future increases in emissions.