Abstract Plant‐mediated CH 4 emission is an important part of the ecosystem CH 4 emission from vegetated wetlands. Inundation depth may alter the potential magnitude of CH 4 releases by changing CH 4 production and plant transport, but the relationships between plant‐mediated CH 4 emissions and inundation depth are still uncertain, especially for estuarine wetlands with changeable hydrological processes. Besides, there are conflicting results regarding the role of inundation depth in plant‐mediated CH 4 emissions. Here we conducted a novel inundation depth experiment (0, 5, 10, 20, 30 and 40 cm inundation depth) dominated by Phragmites australis in the Yellow River estuary, China. Soil CH 4 emissions, ecosystem CH 4 emissions, net ecosystem CO 2 exchange (NEE), soil organic carbon (SOC) and plant traits were measured during the growing seasons of 2018, 2019 and 2020. Plant‐mediated CH 4 emissions were the difference between ecosystem CH 4 emissions and soil CH 4 emissions. The results showed that inundation depth decreased soil CH 4 emissions but increased ecosystem CH 4 emissions. Plant‐mediated CH 4 transport from Phragmites australis accounted for 99% of total ecosystem CH 4 emissions under different inundation depths. Inundation depth strongly stimulated plant‐mediated CH 4 emission from 0 to 20 cm during the growing seasons. The increased NEE enhanced plant‐mediated CH 4 emissions by altering production, suggesting that carbon components derived from photosynthetic carbon input may benefit CH 4 production. Additionally, the increased plant height promoted CH 4 emission by regulating plant transport, indicating that plant traits may play an important role in transport of CH 4 . Our findings indicated that NEE and plant height play an important role in plant‐mediated CH 4 emissions under different inundation depths in estuarine wetland. This study also highlights that hydrological regimes and plant traits are essential for the estimation of CH 4 emissions in future projections of global wetland changes. Read the free Plain Language Summary for this article on the Journal blog.