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We used a process-based model to examine the role of spatial heterogeneity of surface and sub-surface water on the carbon budget of the wetlands of the West Siberian Lowland over the period 1948–2010. We found that, while surface heterogeneity (fractional saturated area) had little overall effect on estimates of the region's carbon fluxes, sub-surface heterogeneity (spatial variations in water table depth) played an important role in both the overall magnitude and spatial distribution of estimates of the region's carbon fluxes. In particular, to reproduce the spatial pattern of CH4 emissions recorded by intensive in situ observations across the domain, in which very little CH4 is emitted north of 60° N, it was necessary to (a) account for CH4 emissions from unsaturated wetlands and (b) use spatially varying methane model parameters that reduced estimated CH4 emissions in the northern (permafrost) half of the domain (and/or account for lower CH4 emissions under inundated conditions). Our results suggest that previous estimates of the response of these wetlands to thawing permafrost may have overestimated future increases in methane emissions in the permafrost zone.