Methane production, transport and emission in a floodplain lake in central Amazonia were investigated by isotopic studies and gas exchange measurements. Samples of sediment free gas were depleted in δ13CCH4, δ13DCH4,and δ13CCO2 values. The isotopic composition of the sediment free methane clearly demonstrated a methane production by methyl fermentation. This finding was strengthened by the coexisting δ13CCO2 and δ13CCO2 values in the sediment free gas. The flux rates of methane ebullition and diffusion were measured during a complete annual cycle using the static chamber method. Significant differences were observed in the release of methane from individual vegetation types, i.e., phytoplankton, floating grass mats, and flooded forest. Each vegetation type showed a distinct seasonal pattern. The highest ebullition rates (mean value, 69 mg CH4 m−2d−1) were recorded in the flooded forest, covering the higher areas of the floodplains with a long subaerial period. Significantly lower averages of the gas bubble flux were recorded in the permanently aquatic areas of the lake (mean value, 29 mg CH4 m−2d−1) and in the intermediate area with floating grass mats (mean value, 23 mg CH44 m−2d−1. Ebullition was the predominant mechanism for the methane transport from the varzea sediment into the atmosphere with maximum values of up to 200 mg CH4 m−2d−1. The diffusive flux remained below 29 mg CH4 m−2d−1 at all sites throughout the entire annual cycle. The variation of the ebullutive flux was found to determine the spatial and temporal variation of the total methane flux in the varzea. We estimate that ebullition accounts for 80% of the total methane emission from the varzea.