The impacts of climate change on the world's large lakes are a cause for concern^{1, 2, 3, 4}. For example, over the past decades, mean surface water temperatures in Lake Superior, North America, have warmed faster than air temperature during the thermally stratified summer season, because decreasing ice cover has led to increased heat input^{2, 5}. However, the effects of this change on large lakes have not been studied extensively⁶. Here we analyse observations from buoys and satellites as well as model reanalyses for Lake Superior, and find that increasing temperatures in both air and surface water, and a reduction in the temperature gradient between air and water are destabilizing the atmospheric surface layer above the lake. As a result, surface wind speeds above the lake are increasing by nearly 5% per decade, exceeding trends in wind speed over land. A numerical model of the lake circulation suggests that the increasing wind speeds lead to increases in current speeds, and long-term warming causes the surface mixed layer to shoal and the season of stratification to lengthen. We conclude that climate change will profoundly affect the biogeochemical cycles of large lakes, the mesoscale atmospheric circulation at lake–land boundaries and the transport of airborne pollutants in regions that are rich in lakes.