Abstract End of summer stratification and onset of ice‐on are shifting later across the mid‐latitudes, but the lake‐specific and climatic drivers of lake thermal structure in autumn remain unclear. We used high‐frequency water temperature data (2007–2021) from nine sub‐alpine (>600 m ASL) lakes in the Northeastern US to investigate the drivers and coherence of ecologically important autumn processes. The end of summer stratification was highly variable across lakes and mediated by DOC and lake depth. The timing of end of stratification affected the onset of continuous autumn mixing; however, mixing was decoupled from ice‐on. Ice‐on was highly coherent and driven by air temperature. Extreme weather events with high winds, heavy precipitation, and anomalous air temperatures drove early onset of mixing, re‐stratification events, and freeze‐melt events. The variability of thermal structure during autumn demonstrates that climate change will not uniformly shift the start and end of autumn season later in the year.

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