The Trempealeau National Wildlife Refuge, five miles northwest of Trempealeau, offers a unique opportunity to explore a variety of river, prairie, and bottomland forest habitats. There are numerous interpretive hiking trails and a five-mile self-guided circle drive thought the refuge that is convenient for autos and bikers. In the forested portion, look for hawks, ruffed grouse, cuckoos, yellow breasted chat and bluebirds. Grebes, bitterns, rare double-crested cormorants, geese, ducks, and osprey all nest in the refuge. There is access for canoers who will enjoy very quiet wetland passages. Only hand-powered boats or those with electric motors are allowed in the refuge.

The Great River State Bike Trail passes directly through Trempealeau County. North takes you to the Trempealeau National Wildlife Refuge; south takes you all the way to LaCrosse. A parking lot and facilities make Trempealeau a great place to start your trek. This trail offers a unique opportunity to bike through the Black River bottoms. Listen for sandhill cranes. Birding and wildlife watching opportunities abound. Bring your binoculars! There are nearly 140 miles of level, well maintained bike paths located within the interconnecting trails of Western Wisconsin and the Mississippi River Valley.