Significant change in global climate could occur due to human‐induced changes in the chemistry of the atmosphere. We provide a basis for the continuing assessment of potential impacts of climate change on aquatic ecosystems. A series of climate change scenarios have been developed for the Great Lakes Basin using general circulation models (GCMs), climate spatial transpositions, and historical climate analogs. The direct impacts of climate change on the Great Lakes ecosystem would occur through higher air and water temperatures. Indirect climate change impacts include both positive and negative changes in precipitation, decreases riverine runoff, less snowfall and snowpack accumulation, higher evapotranspiration, and a reduction in lake levels and connecting channel flows. These climate and hydrologic changes affect the quantity and quality of wetland and aquatic habitats, alter the frequency and timing of lake turnover, and change dissolved oxygen, and alter fish community composition and dynamics. We provide an integration of Great Lakes climate scenarios. We also illustrate, for the first time, the spatial variability of the climate change scenarios on a tributary river‐basin scale.