Future changes to climate in the Great Lakes may have important consequences for fisheries. Evidence suggests that Great Lakes air and water temperatures have risen and the duration of ice cover has lessened during the past century. Global circulation models (GCMs) suggest future warming and increases in precipitation in the region. We present new evidence that water temperatures have risen in Lake Erie, particularly during summer and winter in the period 19652000. GCM forecasts coupled with physical models suggest lower annual runoff, less ice cover, and lower lake levels in the future, but the certainty of these forecasts is low. Assessment of the likely effects of climate change on fish stocks will require an integrative approach that considers several components of habitat rather than water temperature alone. We recommend using mechanistic models that couple habitat conditions to population demographics to explore integrated effects of climate-caused habitat change and illustrate this approach with a model for Lake Erie walleye (Sander vitreum). We show that the combined effect on walleye populations of plausible changes in temperature, river hydrology, lake levels, and light penetration can be quite different from that which would be expected based on consideration of only a single factor.