Purpose <p>Spring-fed wetlands are a wide category of natural wetlands. However, information on methane (CH₄) fluxes and their influencing variables is rarely known in spring-fed wetlands, and should therefore be prioritized for additional research. In this study, in situ CH₄ emissions and their relationships with biotic and abiotic variables were observed and determined in a spring-fed wetland of the arid and semi-arid region in northern China.</p> Methods <p>In situ CH₄ emissions were mainly determined by the method of static closed-chamber plus gas chromatography.</p> Results <p>Overall CH₄ emissions were observed at 6.9 ± 2.9 mg m^− 2 h^− 1 (<i>n</i> = 5 habitats) in the wetland from November 2019 to December 2019 and from June 2020 to June 2021. Substantial CH₄ was dominantly emitted by plant-mediated transport in the growing seasons. Water level slightly fluctuated throughout the growing seasons due to the adjustment of spring outpouring, a prominent feature of the wetland, but it largely fluctuated during intermittent flooding. CH₄ emissions were significantly correlated with air/soil temperatures at seasonal and annual scales.</p> Conclusion <p>CH₄ emissions in this spring-fed wetland were much higher in the growing than non-growing seasons, which can be mainly explained by the effects of plant species and temperature. The vast numbers of spring-fed wetlands are threatened by climate warming, highlighting the need for further research on their potential implications for the CH₄ budgets of arid and semi-arid regions.</p> Graphical abstract <p></p>