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Abstract Winter ice conditions in the Great Lakes play a crucial role in shaping ecological processes, shoreline dynamics, and regional weather patterns. Although atmospheric factors are widely acknowledged as the primary drivers of ice formation and duration, the influence of subsurface groundwater flow remains largely unexplored. In this study, we evaluate how spatially and temporally variable groundwater flux affects ice formation and thermal structure in Lakes Michigan and Huron, using a coupled hydrodynamic‐ice model. Simulations were conducted for the winters of 2014, 2015, and 2016—a period characterized by distinct atmospheric and ice conditions—and were validated against observed ice concentration maps and temperature profiles. Results show that groundwater enhances ice thickness during colder winters by strengthening water column stability, limiting vertical mixing, and insulating the surface layer, thus promoting thicker, longer‐lasting ice. Sensitivity analyses reveal that moderate increases in groundwater flux intensify stratification and prolong ice concentration, while an extreme, high flux (1000x) disrupts stability and reduces ice thickness. Coastal regions display more pronounced effects due to higher groundwater input, whereas offshore zones exhibit comparatively weaker responses. These findings highlight the significant role of groundwater flux in modulating ice dynamics and stratification in large freshwater systems such as the Great Lakes. This research underscores the importance of incorporating subsurface hydrology into coupled modeling frameworks to improve predictions of ice dynamics and water column stratification. Future work should focus on obtaining high‐resolution observational data on groundwater flux and ice thickness, particularly near shorelines, to further refine coupled hydrodynamic‐ice models.