Mississippi River water trails

Winona to Fountain City

Get the real flavor of Mississippi River paddling with a day trip to Fountain City. This route takes you through a wonderful maze of islands and channels and out into some big water near Fountain City. Before setting out, pick up a map of Pool 5A from the U.S. Fish and Wildlife Service.

Upper Mississippi River National Wildlife & Fish Refuge

Most of the backwater shores and islands on the Mississippi River near Winona are part of the Upper Mississippi River National Wildlife & Fish Refuge. The refuge extends 261 miles from the mouth of the Chippewa River near Nelson, Wisconsin, to just above Rock Island, Illinois, and covers 194,000 acres of islands, bottomlands and shoreline. Most Refuge lands are marked with the U.S. Fish & Wildlife Service’s “blue goose” signs. For a complete listing of Refuge regulations, or to get a free Pool Map, visit or call the Winona U.S. Fish & Wildlife Service office at 51 East Third Street, Winona, MN 55987 (507) 454-7351.

Begin your trip at Upper McNally Landing or Verchota Landing on Prairie Island. Follow Pap Slough from upper Polander Lake upstream until it opens into the Main Channel just below Fountain City.When you reach the Main Channel you must hug the shore. Choose which side of the river to stay on based on conditions of the current and the wind. Be alert to the current or the sudden appearance of a tow. Don’t cross the channel if a tow is approaching. Head for the landing and dock on the upstream end of downtown Fountain City. On your return trip, cut across the Main Channel to the small island a little upstream. Follow the current down Honeymoon Slough, which is near the island. It will take you back to upper Polander Lake just above Pap Slough.

Whitman Bottoms

The Whitman Bottoms, just above Fountain City, is a stretch of wild, heavily wooded backwater threaded with a maze of channels. This state wildlife area is a great place to see how the Mississippi looked before the dams. To get to Whitman you can put in at Merrick State Park or just upstream from Merrick on Indian Creek Rd. Note your route carefully to avoid getting lost.

Long Lake Canoe Trail

For an enjoyable afternoon, try the Long Lake Canoe Trail. The trail is located below Lock & Dam 6 at Trempealeau. From highway 35 in Trempealeau, go south on Fremont St. (Lake Rd.), continue past the railroad tracks 1.5 miles to Long Lake landing, the trailhead. The well-marked loop meanders for about 4.5 miles through a backwaters and a short stretch on the Main Channel.

Voyageurs Canoe Trail (Perrot State Park)

This marked 3.4 mile loop takes you through Trempealeau Bay and past Trempealeau Mountain in an enclosed backwater in Perrot State Park. Enquire at the park office about canoe rentals.

Winona to Trempealeau

For a relaxing paddle, follow the wide-open river in an easy downstream route to Trempealeau, and arrange to have someone pick you up there. This day-long trip takes you past islands and sloughs where the river is broad with beautiful views of the surrounding bluffs. Put in at the landing at Latsch Island beach and simply hold to the left until you reach the railroad dike, then follow it downstream. Trempealeau Mountain, the only bluff completely surrounded by water, greets you just upstream from the town of Trempealeau. You can pull out here if you cut left under the railroad bridge and use the landing at Perrot State Park. To reach the landing in Trempealeau, continue on and hold close to the left shoreline to avoid tows heading for Lock & Dam 6.

Trempealeau River

The Trempealeau River twists through farmland and rich bottoms that are home to a great variety of wildlife. For a day trip on the Trempealeau, put in at the Sportsman’s Park in Dodge, and follow the stream down through the Trempealeau National Wildlife Refuge to the landing on West Prairie Rd at the main entrance to the Refuge. This river can be challenging due to downed trees and snags in the water, and the current is swift in places. You must be able to maneuver your boat quickly to avoid trouble.

Root River

The Root River flows through a pastoral valley rimmed with limestone bluffs. This river can be an easy or a challenging paddle depending upon water levels and condition. A trip on the Root can be long or short. There are landings located all along the river, so it’s easy to get on and off the water where you want. Designated canoe campsites on the riverbank allow you to turn a day trip into an overnight camp out. Free Root River Canoe maps are available from the Minnesota Department of Natural Resources by calling (888) 646-6367.