Abstract Global surface freshwater primarily resides in lakes, with the overwhelming majority found in Earth’s largest lakes, thus understanding potential climate change effects in these large lakes is critical. In dimictic lakes, climate change has extended the duration of summer thermal stratification and reduced the length of the ice season. These changes are relatively straightforward to evaluate in smaller, inland lakes. However in large lakes, such as the North American Great Lakes, temporally intermittent and spatially heterogeneous ice cover, and spatial thermal heterogeneity limit the utility of simple ice on-off or mixing classifications; therefore, assessing how climate change is impacting winter conditions in large lakes is challenging. Here, we use in-situ and satellite-derived surface water temperature observations from the North American Great Lakes to overcome these limitations and show that warming air temperatures are driving reductions in the number of winter days, collectively those with either ice cover or inverse thermal stratification, in favor of increases in isothermal conditions for the period 1995 to 2023. We find that on average the Great Lakes are experiencing a loss of 14 winter days per decade. Our results demonstrate how climate change has yielded disproportionate changes in the annual thermal cycle and mixing conditions of Earth’s largest freshwater system and signals the potential for fundamental ecosystem shifts due to a loss of winter.