The rock that makes up the Tobermory landscape is dolostone, laid down 400 million years ago in a warm, shallow sea. Coral reefs flourished, growing upwards and expanding into dome shaped mounds called bioherms. Bears Rump Island and each of the bluffs of Flowerpot Island are all ancient bioherms. They are also evident on a smaller scale along the Georgian Bay shoreline between Tobermory and Halfway Rock Point. Between the bioherms, layers of sediment built up into vast inter-reefal planes which have since hardened into what is called dolostone pavement. In some areas of the lake bed the pavement remains intact while in other places it has broken off in layers into various sizes of rock pieces.
One million years ago, the climate in the northern latitudes began to cool and the areas of bioherms and dolostone pavement were scraped and scoured by four waves of glaciers, the last one beginning thirteen thousand years ago. The dramatic results of a 1.6 kilometer thick wall of ice advancing over the area are evident in the rock. Striations in the dolostone pavement indicate that the glaciers traveled across this area from northeast to southwest. A few meters south and west of the wreck of the W. L. Wetmore is an area of larger glacial grooves, some of which are 1.5 meters deep and run for hundreds of meters. Glacial erratics, usually granite boulders carried to this area from the Canadian Shield are common.
When the climate moderated about six thousand years ago, the melting glaciers retreated leaving vast glacial lakes behind, submerging the Bruce Peninsula. Since then, the lake levels have been dropping, forming sea stacks (flowerpots) and sea caves in the process. The caves began to form as water percolated through fractures in the rock, dissolving out rounded passages. As the water level continued to drop the passages were enlarged by waves and freeze-thaw action. The caves just west of Halfway Rock Point are a good illustration of the process.
Another geological feature abundant in the Tobermory area is the pitting of the rock surface, giving it a Swiss cheese appearance. Underwater pitting is caused by the growth of algae which excretes acids that dissolves the rock creating these pits.