Bay Harbor is in a sheltered bay on the south shore of the Little Traverse Bay on Lake Michigan. It is on U.S. Route 31, with Petoskey, immediately adjacent to the east along the harbor. It is home to the upscale Inn at Bay Harbor, a Boyne Resort property. Bay Harbor is an unincorporated upscale residential and resort community in Emmet County in the U.S. state of Michigan. It is a partially-gated, master-planned community.