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If you plan to paddle the entire 261 river mile refuge, you will need to know how to go through the locks. Those unfamiliar with the lockage process should review Locking Through: The Key to Use of Navigational Locks
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| Pool | Canoe Trail/Areas | Directions | Length | Skill Level |
| Pool 4 | Nelson Trevino | From Nelson, Wisconsin, take Highway 25 west towards Wabasha, Minnesota. The Nelson/Trevino Landing is located on the north side of Highway 25 and the Pontoon Slough Landing is located on the south side of Highway 25. | 4.8 miles | Moderate. There is a stretch where you will be paddling against the current. During high water and windy days it will require strong paddling. |
| Pool 5 |
*This is best during high water. The portage is approximately 1/4 mile during low water. |
From Kellogg, MN, take HWY 61 north, turn right onto County road 81, turn left onto County Road 30, turn right onto County Road 24, continue onto N County Road 24, turn right onto Prairie Lane, turn right onto Pioneer Drive. You can access either using the Minnesota DNR Canoe Access area or Pioneer Landing. | 5.2 miles | Moderate. There are two loops, a shorter 1 mile loop or the longer 5.2 mile loop. During low or "normal" pool conditions you will need to portage your canoe between 1st Lake and Wiggle Waggle Slough. This trail winds through the braided streams and sloughs of the Upper Mississippi River. |
| Pool 5 |
Halfmoon Lake | From Kellogg, MN take Hwy 61 south, turn left onto County Road 84, turn right onto West Newton Road, turn right into Halfmoon Landing. | 5 miles | Moderate to Difficult. Difficult during high water. Murphy's cut can be impassable during high water. Difficult due to vegetation towards end of summer. Recommended for experienced paddlers. |
| Pool 5A | Straight Slough | From Winona, MN, take Prairie Island Road to Verchota Landing. |
11 miles | Difficult. The length of this trail makes it a more difficult adventure and you will be going against the current in the beginning. Recommended for experienced paddlers. |
| Pool 7 | Long Lake |
From Trempealeau, WI at the intersection of Highway 35 and Fremont Street, head south on Fremont Street (Lake Road), past the railroad tracks 1.5 miles to the Long Lake Landing. |
5 miles |
Easy. This is a looped trail out of Long Lake Boat Landing. It can take 3-4 hours to complete. It is located in the backwaters, which has slower moving water than the main channel. |
| Pool 7 | Brown's Marsh Canoe Area |
From Onalaska, WI take Highway 35 North , turn left onto County Road OT. Turn left onto County Road ZN, turn right onto County Road Z. Follow County Road Z to the end of the road where you can launch at Lytle’s canoe access point. This is also the parking lot for the Great River State Trail (biking/hiking). | Canoe Area - no marked trails | Easy. This part of the river feels like you are paddling in a shallow lake. Aquatic vegetation is thick in some areas and the water can be quite shallow in places. In some places there are floating mats of vegetation that make navigation difficult. This is designated an Electric Motor Only area. These areas are closed year-round to all motorized vehicles and watercraft except watercraft powered by electric motors or non-motorized means. |
| Pool 8 | From La Crosse, WI take Highway 35 South to County Highway GI (west), the road into Goose Island County Park. The canoe trail may be accessed from any of the four boat ramps in Goose Island County Park. | 7 miles | Moderate. It can take 4-5 hours to complete.You will be paddling against the current for one-half of your trip. You may encounter strong currents, especially during high water events. Canoes rentals available from Goose Island County Park. |
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| Pool 9 | Reno Bottoms | The trail is located off Highway 26, just east of Reno, Minnesota. Be prepared to carry your gear from the parking lot, across the railroad tracks, down to the launch site on the south side of Lock and Dam 8 spillway. |
3 miles to 14 miles | Moderate. There are 3 take-out points along the trail. However, from April to early Reno to New Albin Landing 14 miles (4-8 hours) See below for description of the stretches of river. Spillway to Millstone Landing 7miles (2-4 hours) Pickerel Slough merges with the Millstone to Visger's Landing 3 miles (1-2 hours) During high water you will be able to Visger's to New Albin Army Road Landing 4 miles (1-2 hours) The trail crosses large expanses of open water. Be aware of wind
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| Pool 10 | Ambrough Slough Canoe Area | From Prairie du Chien, WIsconsin head north on WI-35/Great River Road, turn left onto County Road K, take the first right toward Ambro Road. | Area - no marked trails. | Easy. A quiet backwater area to paddle around. |
| Pool 10 | Johnson Slough | From McGregor, Iowa take Hwy 18 south to County Road X56, turn left into the Sny Magill Unit of Effigy Mounds National Park and follow to Sny Magill River access. | 6.1 miles | Moderate. You will paddle against the current for half of this trail. The trail follows the edge of the main channel for approximately 3 miles. |
| Pool 10 | Wyalusing State Park |
From Prairie du Chien, Wisconsin, head south on US Highway 18 and State Highway 35, turn west on County Road C just south of the Wisconsin River bridge. Turn right on County Road X and go one mile to the park entrance, follow signs to boat landing. | 9 miles | Easy. You will paddle through Wood Yard Slough to the main channel of the Mississippi River. The trail then cuts back up the slough to return to the landing. It does require some paddling effort, especially on the last stage.
Wood ducks, pileated woodpeckers and other water birds are common. Canoes can be rented from the Wyalusing State Park concession. |
| Pool 14 | Rock Creek Canoe Loop |
From Camanche, Iowa take HWY 67 south to Rock Creek County Park. | 5.3 miles | Easy. This is a looped trail. |
| Pool 14 | Lost Lake Canoe Loop | From Camache, Iowa take HWY 67 south to Rock Creek County Park. | 2.9 miles | Easy. This is part of the Rock Creek Canoe trails. |
| Pool 14 | Wapsipinicon River Canoe Trail | From Princeton head north on HWY 67. There is an access to the Wapsipinicon River off of Hwy 67. | 10+ miles | Experienced Canoers. One way trip. Launch on Hwy 67 paddle down the Wapsipinicon River and head north on the Mississippi River into the Rock Creek Canoe Loop. |


