Permafrost affects about 24% of the Northern Hemisphere land surface. Organic carbon storage in soils and deep deposits in these regions exceeds 1000 Pg and has resulted in a long-term carbon sink to the atmosphere. A large portion of this carbon is perennially frozen and radiocarbon dates ranging from Holocene to Late Pleistocene ages indicate it has been removed from active cycling for thousands of years. In a warming Arctic, understanding how short-term processes and their feedbacks with climate might interfere with long-term permafrost soil carbon storage is of crucial importance to projecting future trajectories of climate. For example, complex landscape and biogeochemical dynamics in northern wetlands and lake-rich regions may lead to decomposition of soil organic carbon under anaerobic conditions and significant methane release to the atmosphere. Here we focus on the role of lakes in permafrost regions for the mobilization of old organic carbon from permafrost deposits in the form of methane. Lake cover is especially extensive (up to 40% limnicity) in northern permafrost lowlands associated with thick ice- and organic-rich deposits. A large portion of these lakes are thermokarst lakes that rapidly thaw underlying and surrounding permafrost soils, providing organic-rich anaerobic environments for methane production in thaw bulbs and lake sediments. However, various other types of lakes exist and multiple drivers affect how and at what rates various lake types may interact with permafrost and soil organic carbon. We discuss new broad-scale remote sensing, spatial data analysis, and modeling approaches that allow an assessment of the methane emission potentials of northern high latitude lakes in relation to permafrost and surface deposits.