There is a strong Aboriginal presence in the Southern regions of the Canadian Shield dating from 11,000 years ago. Evidence of settlements have been found on Manitoulin Island and near Killarney. At the time of European contact, the Ojibwe and Ottawa First Nations, both of whom call themselves Anishinaabe, lived along the Northern, Eastern and Western shores of Georgian Bay. The Huron and Tionontati inhabited the lands along the Southern coast, having migrated from the northern shores of Lake Ontario. Names of islands such as "Manitoulin" and "Giant's Tomb" are evidence of the richness of the cultural history of the area. Aboriginal communities continue to live on their territories and practice their cultural traditions.
The first European people to visit the area was in1610 with the Onontchataronon, an Algonquian people of the Ottawa River. They traveled every winter to live with the Arendarhonon people of the Huron confederacy at the Southern end of Georgian Bay, in the area now called "Huronia".
In 1615 the French explorer Samuel de Champlain, made a visit to Georgian Bay and overwintered in Huronia. He was preceded that summer by a Récollet missionary, Joseph Le Caron, who would live among the Huron in 1615–1616 and 1623–1624. Another Récollet missionary, Gabriel Sagard, lived there from 1623–34. The French Jesuit Jean de Brébeuf began a mission in Huronia in 1626. In 1639 he oversaw the building of the mission fort of Sainte-Marie, Ontario's first European settlement, at what is now the town of Midland. The reconstructed Jesuit mission, Sainte-Marie among the Hurons, is now a historic park operated by the province of Ontario.
Nearby is the Martyrs' Shrine, a Catholic church dedicated to the Canadian Martyrs, Jesuits who were killed during Iroquois warfare against the Huron around Georgian Bay in the 17th century. Penetanguishene, an Ojibwe village located at the Southern tip of the bay near present-day Midland, was developed as a naval base in 1793 by John Graves Simcoe, first Lieutenant Governor of Upper Canada. In 1814, during the War of 1812 between Great Britain and the United States, one of the battles was fought in southern Georgian Bay. On August 17, at the mouth of the Nottawasaga River near Wasaga Beach, the British schooner HMS Nancy was sunk by three American vessels. Several weeks later, Nancy was avenged when British boarding parties in the De Tour Passage surprised and captured two of the three American vessels. Georgian Bay was first charted in 1815 by Captain William Fitzwilliam Owen, who called it Lake Manitoulin. Captain Henry Bayfield, who made more detailed charts of the bay, renamed it in 1822 after King George IV. His charts are the basis of those in use today.