Predicted climate-induced changes in the Great Lakes include increased variability in water levels, which may shift periphyton habitat. Our goal was to determine the impacts of water level changes in Lake Superior on the periphyton community assemblages in the Keweenaw Peninsula with different surface geology. At three sites, we identified periphyton assemblages as a function of depth, determined surface area of periphyton habitat using high resolution bathymetry, and estimated the impact of water level changes in Lake Superior on periphyton habitat. Our results suggest that substrate geology influences periphyton community assemblages in the Keweenaw Peninsula. Using predicted changes in water levels, we found that a decrease in levels of 0.63 m resulted in a loss of available surface area for periphyton habitat by 600 to 3000 m2 per 100 m of shoreline with slopes ranging 2 to 9°. If water levels rise, the surface area of substrate will increase by 150 to 370 m2 per 100 m of shoreline, as the slopes above the lake levels are steeper (8–20°). Since periphyton communities vary per site, changes in the surface area of the substrate will likely result in a shift in species composition, which could alter the structure of aquatic food webs and ecological processes.