Abstract. In thermally stratified lakes, the greatest annual methane emissions typically occur during thermal overturn events. In July of 2012, Greenland experienced significant warming that resulted in substantial melting of the Greenland Ice Sheet and enhanced runoff events. This unusual climate phenomenon provided an opportunity to examine the effects of short-term natural heating on lake thermal structure and methane dynamics and compare these observations with those from the following year, when temperatures were normal. Here, we focus on methane concentrations within the water column of five adjacent small lakes on the ice-free margin of southwestern Greenland under open-water and ice-covered conditions from 2012–2014. Enhanced warming of the epilimnion in the lakes under open-water conditions in 2012 led to strong thermal stability and the development of anoxic hypolimnia in each of the lakes. As a result, during open-water conditions, mean dissolved methane concentrations in the water column were significantly (p < 0.0001) greater in 2012 than in 2013. In all of the lakes, mean methane concentrations under ice-covered conditions were significantly (p < 0.0001) greater than under open-water conditions, suggesting spring overturn is currently the largest annual methane flux to the atmosphere. As the climate continues to warm, shorter ice cover durations are expected, which may reduce the winter inventory of methane and lead to a decrease in total methane flux during ice melt. Under open-water conditions, greater heat income and warming of lake surface waters will lead to increased thermal stratification and hypolimnetic anoxia, which will consequently result in increased water column inventories of methane. This stored methane will be susceptible to emissions during fall overturn, which may result in a shift in greatest annual efflux of methane from spring melt to fall overturn. The results of this study suggest that interannual variation in ground-level air temperatures may be the primary driver of changes in methane dynamics because it controls both the duration of ice cover and the strength of thermal stratification.