The Great Lakes of northern Canada are relatively understudied ecosystems in comparison to the better-investigated Laurentian Great Lakes. This chain of lakes extends north from Lake Winnipeg (a shallow prairie lake) to Wollaston Lake and Lake Athabasca (moderately deep arboreal lakes) to Great Slave Lake (a deep subarctic lake) to Great Bear Lake (a deep lake located in the Arctic Circle). Many of these lakes have experienced minor localized anthropogenic impacts. Impacts include mining and fishing in the north and agricultural and urban impacts in the south. While most of these lakes are located in the relatively undeveloped regions of Canada, the northward migration of natural resource-based industries such as forestry, mining, agriculture and oil and gas operations may potentially affect their ecosystem health. Research programs are required to better understand the natural features of these ecosystems to further protect them from anthropogenically driven change. Long-term monitoring programs are also required to protect fish, water quality and other ecosystem features. An emerging problem is meeting northern community concerns with environmental protection while providing the economic base for an increasingly modern lifestyle.