The nearshore zones of the Great Lakes provide essential habitat for biota and are perhaps the region of the lakes most susceptible to human impacts. The objective of our study was to develop a fish habitat classification for the nearshore zone of Lake Ontario based on physical characteristics of that zone, land cover in the surrounding watershed, and fish community patterns. Nearly 80% of the spatial variation in fish community data was described by 2 physical variables (average fetch and bathymetric slope of the nearshore zone) and 2 land-cover variables (urban/industrial development and mixed forest cover) in adjacent watersheds. These variables are likely to be surrogates for other conditions in the nearshore, such as wave action, circulation, vegetation, and water quality. A 12-group fish habitat classification was developed from those variables. Validation and significance tests identified similarities and differences among the fish communities in the classes and indicated that the number of classes should be collapsed to 3: exposed, sheltered, and developed/urbanized. In general, the western basin of the lake was developed, the central region was exposed, and the eastern region of the lake was a mix of exposed and sheltered classes. These results highlight that even in lakes as large as Lake Ontario, the nearshore fish community is influenced by watershed land cover, and emphasize that management or restoration of the nearshore ecosystem in lakes will require integration of aquatic, watershed, and land-cover management.