The waters of the Arctic Archipelago Ecozone wash the shores of three provinces and two territories. Biologically, it is as least as productive as the adjacent lands. Canada's Inuit find most of their traditional food in this ecozone, so hunting and fishing remain significant human activities. While it is common to think of the arctic in the context of European explorers, the Inuit have a rich and varied culture that well predates their involvement. Arctic Char and Greenland Halibut (turbot) support commercial fisheries in Baffin Bay. Oil and gas exploration and development provide economic opportunities but still continue to pose environmental threats to the ecozone, especially in the Beaufort Sea. As mineral prospectors gain more experience in northern latitudes, large mineral deposits may be found, raising questions about mine waste and tailings that could find their way into the sea.

To the south, it seems inevitable that hydroelectric development will continue on the rivers draining into James Bay. Changes in water flow, salt content, and the presence of heavy metals leached from the soil will have unpredictable consequences for the southern portion of the ecozone. The impacts of urbanization will continue as human populations grow, especially in the more southerly reaches. The long-range transport of pollutants from places as far away as Mexico have impacts on the arctic. PCBs, DDT, and mercury are examples of pollutants affecting this ecozone as well as other parts of the Arctic.