Native American's understood the significance of the Boise Brule River from the 1500's.  When French explorers first visited the Lake Superior region in 1679 they were told of twin rivers, connected by a carrying place, which lead south to a mighty river (later identified as the Mississippi River).  The first of these rivers, the one that flowed toward the north was called the Nemitsakouat by the Dakota.   The Chippewa called the rivers Newissakode (Burnt Wood Point) and Wiskada Sibi (Burnt Pine River).

The French called the first river the Bois Brule.  It is generally accepted that its meaning "burnt wood," refers to the charred remains of timber which stood along the upper reaches of the river in those days -- the relics of frequent forest fires caused by lightning accompanying the summer storms, for which the area is famous.  Another story is that the river is named after Etienne Brule, an interpreter for explorer Samuel de Champlain, although this is doubtful.

In the early 1680's, the second of the two rivers was called Riviere du Tombeau (River of the Grave) when they saw a Native American buried along the river after having been bitten by a rattlesnake.  Early map makers changed the name to Riviera de la Madeline to make it more appealing.  By the late 1680's the river was called  Riviere de Sainte-Croix (Holy Cross).  The first person using this name was possibly a French trader named Nicolas Perrot, who issued a proclamation in 1689 that claimed for the French the interior of North America.

An early French fur trading post that was called Fort St. Croix, was established in the late 1680's either along the two mile portage between the two rivers, or at source of the second river.  This lake was named Lac de la Providence and was later called Upper St. Croix Lake.