Methane fluxes to the troposphere from the three principal habitats of the floodplain of the Amazon River main stem (open waters, emergent macrophyte beds, and flooded forests) were determined along a 1700-km reach of the river during the low-water period of the annual flood cycle (November–December 1988). Overall, emissions averaged 68 (±20) mg CH4 m−2 d−1 and were significantly lower than similar emissions determined previously for the high-water period, 184 (±41) mg CH4 m−2 d−1 (July–August 1986). This difference was due to significantly lower emissions from floating macrophyte environments. Low-water emissions from open waters and flooded forest areas were not significantly different than at high water. A monthly time series of methane emissions from eight lakes located in the central Amazon basin showed similar results. Average annual emission from the lakes was 125 (±28) mg CH4 m−2 d−1. Methane emissions from lakes were significantly higher during the high water period, again primarily due to an increase in emissions from macrophyte habitats. The data were used to calculate a seasonally weighted annual emission to the troposphere from the Amazon River main stem floodplain of 5.1 Tg yr−1, which indicates the importance of the area in global atmospheric chemistry.