We develop a dynamic methanogen-available carbon model (DMCM) to quantify the role of the methanogen-available carbon pool in determining the spatial and temporal variability of tropical wetland CH<sub>4</sub> emissions over seasonal timescales. We fit DMCM parameters to satellite observations of CH<sub>4</sub> columns from SCIAMACHY CH<sub>4</sub> and equivalent water height (EWH) from GRACE. Over the Amazon River basin we found substantial seasonal variability of this carbon pool (coefficient of variation = 28 ± 22%) and a rapid decay constant (φ = 0.017 day<sup>−1</sup>), in agreement with available laboratory measurements, suggesting that plant litter is likely the prominent methanogen carbon source over this region. Using the DMCM we derived global CH<sub>4</sub> emissions for 2003–2009, and determined the resulting seasonal variability of atmospheric CH<sub>4</sub> on a global scale using the GEOS-Chem atmospheric chemistry and transport model. First, we estimated that tropical emissions amounted to 111.1 Tg CH<sub>4</sub> yr<sup>−1</sup>, of which 24% was emitted from Amazon wetlands. We estimated that annual tropical wetland emissions increased by 3.4 Tg CH<sub>4</sub> yr<sup>−1</sup> between 2003 and 2009. Second, we found that the model was able to reproduce the observed seasonal lag of CH<sub>4</sub> concentrations peaking 1–3 months before peak EWH values. We also found that our estimates of CH<sub>4</sub> emissions substantially improved the comparison between the model and observed CH<sub>4</sub> surface concentrations (<i>r</i> = 0.9). We anticipate that these new insights from the DMCM represent a fundamental step in parameterising tropical wetland CH<sub>4</sub> emissions and quantifying the seasonal variability and future trends of tropical CH<sub>4</sub> emissions.