Theodore Roosevelt National Park offers an interesting canoeing/kayaking/rafting exprience along the Little Missouri River which flows through 11 miles of the southern unit of the park.
Warning: There are wildlife barriers that completely cross the river at either end of Theodore Roosevelt National Park that require portages. Float this river at your own risk.

Another option is to float the Little Missouri from the park's South Unit to the North Unit. This is a 110 mile trip and takes several days. Remember, this area has rought terrain so prepare properly for any float. Also, floaters have reported wires and temporary fences crossing the river out of park areas. Float at your own risk. Your safest bet would be to stick inside Theodore Roosevelt National Park, being well aware of the boundaries and avoiding the wildlife barriers.