Waterbodies in the arctic permafrost zone are considered a major source of the greenhouse gas methane (CH4). Spatial extrapolation of these CH4 fluxes to a region or the circum-Arctic, however, are still associated with large uncertainties. Here, we address this issue by using a combination of airborne CH 4 flux measurements and waterbody mapping based on TerraSAR-X and Sentinel-1 data across two study areas (1000 km2) in the Mackenzie Delta, Canada. Our results indicate that permafrost waterbodies, even if they seem to be strong emitters on an individual basis, do not necessarily translate into significant CH 4 emission hot spots on a regional scale. Our results show inconsistent patterns in the correlations between waterbody types and the CH 4 flux in the two study areas and across different spatial resolutions. Technical advances enabling the determination of the CH4 flux of individual waterbodies across a region provide a prospective direction to improve our understanding.