Most of Earth's fresh surface water is consolidated in just a few of its largest lakes, and because of their unique response to environmental conditions, lakes have been identified as climate change sentinels. While the response of lake surface water temperatures to climate change is well documented from satellite and summer in situ measurements, our understanding of how water temperatures in large lakes are responding at depth is limited, as few large lakes have detailed long-term subsurface observations. We present an analysis of three decades of high frequency (3-hourly and hourly) subsurface water temperature data from Lake Michigan. This unique data set reveals that deep water temperatures are rising in the winter and provides precise measurements of the timing of fall overturn, the point of minimum temperature, and the duration of the winter cooling period. Relationships from the data show a shortened winter season results in higher subsurface temperatures and earlier onset of summer stratification. Shifts in the thermal regimes of large lakes will have profound impacts on the ecosystems of the world's surface freshwater.