Waterbodies in the arctic permafrost zone are considered a major source of the greenhouse gas methane (CH ) in addition to CH emissions from arctic wetlands. However, the spatio-temporal variability of CH fluxes from waterbodies complicates spatial extrapolation of CH measurements from single waterbodies. Therefore, their contribution to the CH budget of the arctic permafrost zone is not yet well understood. Using the example of two study areas of 1,000 km² each in the Mackenzie Delta, Canada, we approach this issue (i) by analyzing correlations on the landscape scale between numerous waterbodies and CH fluxes and (ii) by analyzing the influence of the spatial resolution of CH flux data on the detected relationships. A CH flux map with a resolution of 100 m was derived from two aircraft eddy-covariance campaigns in the summers of 2012 and 2013. We combined the CH flux map with high spatial resolution (2.5 m) waterbody maps from the Permafrost Region Pond and Lake Database and classified the waterbody depth based on Sentinel-1 SAR backscatter data. Subsequently, we reduced the resolution of the CH flux map to analyze if different spatial resolutions of CH flux data affected the detectability of relationships between waterbody coverage, number, depth, or size and the CH flux. We did not find consistent correlations between waterbody characteristics and the CH flux in the two study areas across the different resolutions. Our results indicate that waterbodies in permafrost landscapes, even if they seem to be emission hot spots on an individual basis or contain zones of above average emissions, do currently not necessarily translate into significant CH emission hot spots on a regional scale, but their role might change in a warmer climate.