This study presents the hotspot parameterization, a novel approach to upscaling methane emissions in a boreal peatland from the micro-topographic scale to the landscape scale. We based this new parameterization on the analysis of water table patterns generated by the Hummock–Hollow (HH) model. We show how the hotspot parameterization successfully upscales the micro-topographic controls on methane emissions for both present-day conditions and for the next century under three different scenarios.