The Pine River flows along the Minnesota-Ontario border a short distance, primarily within the Boundary Waters Canoe Area Wilderness and La Verendrye Provincial Park. From Gunflint Lake, the river flows north into Magnetic Lake and from there into Clove Lake and finally Granite Lake where it joins the Granite River. The Granite River then continues northward along the border into Saganaga Lake.
By portaging around rapids, the Pine River is navigable by canoe.