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The first records of this area are geological, and written not in books, but in rock layers. A succession of immense seas, live volcanoes and mountain ranges left evidence of their passing before the glacial period. During the glacial period four great glaciers moved over this area. During the melting of the fourth and final glacier, the Minnesota River and Glacial Lake Agassiz came into being. As the vast lake, larger than all the Great Lakes together, retracted, it carved the Minnesota River as its turbulent outlet, digging a path toward the Mississippi River basin. Almost certainly human beings were here near the end of the glacial period and their descendants dominated the area until the 18th Century.

History records indicate that two large Indian nations were located in the Minnesota state region. The Dakota, or Sioux, Indian nation had three large divisions, and the Santee Indians resided in this area as early as the 1600's. The Dakota were challenged in the 1700's by the westward migration of the Chippewa, and were eventually pushed toward the south and west. Records indicate skirmishes between the Chippewa and members of Chief Shakopee's village from the Minnesota River during 1768 and 1775. By 1839, the village was located east of the present site of the City of Shakopee. Commonly called Teenatahotonwa ("village of the prairie"), it was a village of summer bark lodges, winter tipis, and corn fields with the river serving as natural protection from the Chippewa to the north.

As incoming white explorers moved into the area, they made use of the natural route provided by the Minnesota River. Pierre Charles le Sueur traveled on the Minnesota River in 1700. As le Sueur, Jonathan Carver, Peter Pond, Major Stephen Long, George Catlin and George Featherstonhaugh surveyed, studied and traveled down the Minnesota, they would have passed through the area of modern Shakopee.

In 1844, fur traders Oliver and Harriet Faribault built a cabin of tamarack logs, the first log structure built in the area. The Faribault cabin is now located at a historical site, Murphy's Landing, east of Shakopee. The Reverend Samuel Pond built a cabin just west of Faribault Springs in 1847. He had been invited by Chief Shakopee to mission at his village.

With the signing of the treaties at Mendota and Traverse des Sioux in 1851, the Minnesota Valley was opened to pioneer settlement. The Federal Government acquired roughly 24 million acres of Indian land in exchange for temporary gifts, a trust fund, cash payments and reservations for Sioux tribes. Chief Shakopee's villagers moved to reservations in the upper Minnesota River Valley in the fall of 1853. The Indians held their last festivals at their village and, joined by other bands, moved up the river in a unit of 2,000 on October 12, 1853. Canoes lined the riverbank from today's Lewis Street eastward to Pond's Creek. The younger Chief Shakopee went with his people, but the elder for whom the city is named remained until his death a few years later.