Attempts to reestablish self-sustaining stocks of lake trout (Salvelinus namaycush) in the lower four Great Lakes, where the species was extinguished in the 1950s and 1960s, have been largely unsuccessful. To avoid many of the problems believed to be contributing to this failure, the fishery management community recently established several sanctuaries in the offshore waters of the Great Lakes where the development and protection of self-sustaining stocks of lake trout would be a primary management objective. One of these, the Six Fathom Bank-Yankee Reef sanctuary, was created in the south-central portion of Lake Huron. This sanctuary covers 168,000 ha and includes the shallower portions of the Six Fathom and Ipperwash scarps, which are major bathymetric features in the southern half of the lake. Historical accounts describe Six Fathom Bank as the most important lake trout spawning ground in the lake. Here we present the results of lake bed surveys conducted in the sanctuary with side-scan sonar, underwater videocamera systems, and a small research submarine. Our observations of the lake bed are consistent with what is known of the bedrock stratigraphy, glacial history, and karst geomorphology of the Lake Huron basin. Most of the loose rock we found seemed to be derived from local carbonate bedrock formations, although non-carbonate rock probably from Precambrian sources to the north was also present in some areas. Much of the bedrock and loose rock displayed karst solution features described for the Bruce Peninsula on the Ontario shoreline. Our surveys revealed substantial areas of lake bed at water depths of 20–36 m that resembled suitable spawning and fry production habitat for the shallow-water strains of lake trout that are the focus of the rehabilitation effort. Low mid-lake nutrient levels documented recently by others and the extremely high abundance of Mysis relicta (an important item in the diet of young lake trout) that we documented on Yankee Reef also contributed to our evaluation of the sanctuary as a site with high potential to support a self-sustaining population of lake trout.