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Some of the area was first mapped on birch bark by the Ojibway or Anishinaabe. In 1734, Louis-Joseph Gaultier de La Verendrye was the first European to explore the area during his quest for a route to the Western Sea. Long before the arrival of La Verendrye the area was populated by the Ojibway people, and various other groups before them.

The name of the park is derived from the cowrie shells that were used in ceremonies by the Ojibway, Anishinaabe, and Midewiwin. The historic Winnipeg River and the Whiteshell River are the main rivers that run through this remote park and wilderness area. For thousands of years aboriginal peoples used the area for harvesting wild rice, hunting, fishing, trade, and dwelling. Natives, fur traders, and trappers used the Winnipeg River as a main travel route, along with the Whiteshell River.

Whiteshell Park has many pink granite ridges, cliffs, and flat granite areas used for petroform making by First Nation peoples. There is also archaeological evidence of copper trading, prehistoric quartz mining, and stone tool making in the area. The copper trade, going as far east to Lake Superior, began approximately 4000 years ago. Many artifacts and prehistoric camps were discovered in the Whiteshell Park and are protected under the Heritage Act of Manitoba.