Sources and fluxes of methane to the atmosphere from permafrost are significant but poorly constrained in global climate models. We present data collected from the variable permafrost setting of the outer Mackenzie River Delta, including observations of aquatic methane seepage, core determinations of in situ methane occurrence and seep gas isotope geochemistry. The sources and locations of in situ geologic methane occurrence and aquatic and atmospheric gas release appear to be controlled by the regional geology and permafrost conditions. Where permafrost is >250 m thick, thermogenic gas deposits at depth are isolated by laterally continuous, low permeability ice-bearing sediments with few through-going thawed taliks. Thus, the observed in situ methane and aquatic gas seepage appears to be dominated by microbial methane. In contrast, where permafrost is <80 m thick, taliks are more likely to be through-going, providing permeable conduits from depth and migration pathways for both thermogenic and biogenic gas. Continuous annual fluid sampling of two lakes and a river channel documents aquatic methane flux from microbial sources, more deeply buried thermogenic sources, and mixtures of both. Using estimates of in situ methane concentration from deep core samples and observations of in situ free gas occurrences, we conclude that the reservoir of in situ geologic methane within ice bonded permafrost is substantial and that this methane is presently migrating with ongoing atmospheric release. It is our assessment that the permafrost setting, and processes described are sensitive to future climate change as the permafrost warms.