Among its many impacts, climate warming is leading to increasing winter air temperatures, decreasing ice cover extent, and changing winter precipitation patterns over the Laurentian Great Lakes and their watershed. Understanding and predicting the consequences of these changes is impeded by a shortage of winter‐period studies on most aspects of Great Lake limnology. In this review, we summarize what is known about the Great Lakes during their 3–6 months of winter and identify key open questions about the physics, chemistry, and biology of the Laurentian Great Lakes and other large, seasonally frozen lakes. Existing studies show that winter conditions have important effects on physical, biogeochemical, and biological processes, not only during winter but in subsequent seasons as well. Ice cover, the extent of which fluctuates dramatically among years and the five lakes, emerges as a key variable that controls many aspects of the functioning of the Great Lakes ecosystem. Studies on the properties and formation of Great Lakes ice, its effect on vertical and horizontal mixing, light conditions, and biota, along with winter measurements of fundamental state and rate parameters in the lakes and their watersheds are needed to close the winter knowledge gap. Overcoming the formidable logistical challenges of winter research on these large and dynamic ecosystems may require investment in new, specialized research infrastructure. Perhaps more importantly, it will demand broader recognition of the value of such work and collaboration between physicists, geochemists, and biologists working on the world's seasonally freezing lakes and seas. Plain Language Summary The Laurentian Great Lakes are the world's largest freshwater ecosystem and provide diverse ecosystem services to millions of people. Affected by multiple interacting stressors, this system is the target of extensive restoration and management efforts that demand robust scientific knowledge. Winter limnology represents a key knowledge gap that limits understanding and prediction of the function of the Great Lakes and other large temperate lakes. Here, we summarize what is known about the Great Lakes during their 3–6 months of winter, identify key questions that must be addressed to improve understanding of the physical, chemical, and biological functioning of large lakes in winter, and suggest ways to address these questions. We show that ice cover is a “master variable” that controls numerous aspects of large temperate lake ecology and that the effects of the ongoing reduction in ice cover extent and duration cannot be predicted without improved knowledge of winter limnology. Key Points Winter limnology is a key knowledge gap that limits understanding and management of the Great Lakes and other large, seasonally frozen lakes We review the winter physics, chemistry, and biology of the Great Lakes and identify priority questions for winter research on large lakes Ice cover is a “master variable” for many large lake limnological processes, making a better understanding of its role a research priority