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 CH4 emissions over seasonal timescales. We fit DMCM parameters to satellite observations of CH4 columns from SCIAMACHY CH4 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−1), 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 CH4 emissions for 2003–2009, and determined the resulting seasonal variability of atmospheric CH4 on a global scale using the GEOS-Chem atmospheric chemistry and transport model. First, we estimated that tropical emissions amounted to 111.1 Tg CH4 yr−1, of which 24% was emitted from Amazon wetlands. We estimated that annual tropical wetland emissions increased by 3.4 Tg CH4 yr−1 between 2003 and 2009. Second, we found that the model was able to reproduce the observed seasonal lag of CH4 concentrations peaking 1–3 months before peak EWH values. We also found that our estimates of CH4 emissions substantially improved the comparison between the model and observed CH4 surface concentrations (r = 0.9). We anticipate that these new insights from the DMCM represent a fundamental step in parameterising tropical wetland CH4 emissions and quantifying the seasonal variability and future trends of tropical CH4 emissions.