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The Laurentian Great Lakes are one of the most prominent hotspots for the study of climate change induced lake warming. Warming trends in large, deep lakes, which are often inferred by the observations of lake surface temperature (LST) in most studies, are strongly linked to the total lake heat content. In this study, we use a 3D hydrodynamic model to examine the nonlinear processes of water mixing and ice formation that cause changes in lake heat content and further variation of LST. With a focus on mechanism study, a series of process-oriented experiments is carried out to understand the interactions among these processes and their relative importance to the lake heat budget. Using this hydrodynamic model, we estimate the lake heat content by integrating over the entire 3D volume. Our analysis reveals that (1) Heat content trends do not necessarily follow (can even be opposed to) trends in LST. Hence, using LST as a warming indicator can be problematic; (2) vertical mixing in water column may play a more important role in regulating lake warming than traditionally expected. Changes in the water mixing pattern can have a prolonged effect on the thermal structure; (3) Ice albedo feedback, even in cold winters, has little impact on lake thermal structure, and its influence on lake warming may have been overestimated. Our results indicate that climate change will not only affect the air-lake energy exchange but can also alter lake internal dynamics, therefore, the lake's response to a changing climate may vary with time.