AbstractIn ice‐covered lakes, near‐bottom oxygen concentration decreases for most of the wintertime, sometimes down to the point that bottom waters become hypoxic. Studies insofar have reached divergent conclusions on whether climate change limits or reinforces the extent and duration of hypoxia under ice, raising the need for a comprehensive understanding of the drivers of the dissolved oxygen (DO) dynamics under lake ice. Using high‐temporal resolution time series of DO concentration and temperature across 14 mountain lakes, we showed that the duration of bottom hypoxia under ice varies from 0 to 236 d within lakes and among years. The variability of hypoxia duration was primarily explained by changes in the decay rate of DO above the lake bottom rather than by differences in DO concentration at the ice onset or in the ice‐cover duration. We observed that the DO decay rate was primarily linked to physical controls (i.e., deep‐water warming) rather than biogeochemical drivers (i.e., proxies for lake or catchment productivity). Using a simple numerical model, we provided a proof‐of‐concept that the near‐bed stratification can be the mechanism tying the DO decay rate to the sediment heat release under the ice. We ultimately showed that the DO decay rate and hypoxia duration are driven by the summer light climate, with faster oxygen decline found under the ice of clearer cryostratified alpine lakes. We derived a framework theorizing how the hypoxia duration might change under the ice of alpine lakes in a warmer climate.