To understand the effect of water level on CH4 emissions from an invasive Spartina alterniflora coastal brackish marsh, we measured CH4 emissions from intermittently and permanently (5cm water depth) inundated mesocosms with or without N fertilizer added at a rate of 2.7gNm−2. Dissolved CH4 concentrations in porewater and vertically-profiled sediment redox potential were measured, as were aboveground biomass and stem density of S. alterniflora. Mean CH4 fluxes during the growing season in permanently inundated mesocosms without and with N fertilizer were 1.03 and 1.73mg CH4 m−2 h−1, respectively, which were significantly higher than in the intermittently inundated mesocosms. This response indicates that prolonged submergence of sediment, up to a water depth of 5cm, stimulated CH4 release. Inundation did not greatly affect aboveground biomass and stem density, but did significantly reduce redox potential in sediment, which in turn stimulated CH4 production and increased the CH4 concentration of porewater, resulting in higher CH4 emission in the mesocosm. Our data showed that the stimulatory effect of shallow, permanent inundation on CH4 emission in S. alterniflora marsh sediment was due primarily to an improved methanogenic environment rather than an increase in plant-derived substrates and/or the number of gas emission pathways through the plant’s aerenchymal system.