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Wetlands, and especially their littoral zones, are considered to be CH4 emissions hotspots. The recent creation of reservoirs has caused a rapid increase in the area of the world’s littoral zones. To investigate the effects of water depth and water level fluctuation on CH4 fluxes, and how these are coupled with vegetation and nutrients, we used static closed chamber and gas chromatography techniques to measure CH4 fluxes in the littoral zone of a large reservoir near Beijing, China, from November 2011 to October 2012. We found that CH4 flux decreased significantly along a transect from open water to dry land, from 3.1 mg m−2 h−1 at the deep water site to approximately 1.3 mg m−2 h−1 at the shallow water site, and less than 0.01 mg m−2 h−1 in the non-flooded area. Water level influenced CH4 flux by affecting soil properties including soil redox potential, soil carbon and nitrogen, and bulk density. The largest emission of all was from the seasonally flooded site after a flooding event (up to 21.1 mg m−2 h−1), which may have been caused by vegetation decomposition. Submerged sites had greater emissions, while the driest site had lower emissions. Immediately after the monthly measurements had been made, we removed the aboveground vegetation to enable an assessment of the gas transportation per unit of biomass. Removal of biomass decreased emissions by up to 53%. These results indicated the dominant effect of water depth on CH4 flux through effects of soil conditions, plant species composition and distribution. This study suggests that temporally flooded wetlands, including littoral zones, contribute significantly to the global CH4 burden. However, the current challenge is to capture their spatial extent and temporal variation in the fluxes.