The islands and shorelines of Georgian Bay National Park belong to an area of mixed coniferous and hardwood forest known as the Great Lakes - St. Lawrence Forest Region. It is a transition zone between the hardwood forests which extend into the United States and the boreal forests of the Canadian north. This diverse ecosystem is home to an amazing number of plants and animals.

Glaciers have also left their mark in the park. They scoured the bedrock clean in some places while in others deposited fertile soil that enabled forests to thrive. Many of the depressions carved out by the receding glaciers have filled in with water creating marshes and bogs. The area is also well known for its reptile and amphibian population. Beausoleil Island is one of the last refuges for the seldom seen eastern massasauga; the only snake in Ontario whose venom is poisonous.