The Laurentian Great Lakes Basin provides an ecological system to evaluate the potential effect of climate change on dynamics of fish populations and the management of their fisheries. This review describes the physical and biological mechanisms by which fish populations will be affected by changes in timing and duration of ice cover, precipitation events and temperature regimes associated with projected climate change in the Great Lakes Basin with a principal focus on the fish communities in shallower regions of the basin. Lake whitefish Coregonus clupeaformis, walleye Sander vitreus and smallmouth bass Micropterus dolomieu were examined to assess the potential effects of climate change on guilds of Great Lakes cold, cool and warm-water fishes, respectively. Overall, the projections for these fishes are for the increased thermally suitable habitat within the lakes, though in different regions than they currently inhabit. Colder-water fishes will seek refuge further north and deeper in the water column and warmer-water fishes will fill the vacated habitat space in the warmer regions of the lakes. While these projections can be modified by a number of other habitat elements (e.g. anoxia, ice cover, dispersal ability and trophic productivity), it is clear that climate-change drivers will challenge the nature, flexibility and public perception of current fisheries management programmes. Fisheries agencies should develop decision support tools to provide a systematic method for incorporating ecological responses to climate change and moderating public interests to ensure a sustainable future for Great Lakes fishes and fisheries.