| Mallard Slough | Clark, SD | 18.3 miles | SW |
| Dry Lake Number One | Clark, SD | 27.2 miles | SW |
| Caseys Slough | Clark, SD | 30.5 miles | SE |
| Wolf Slough | Codington, SD | 38.4 miles | SE |
| Stoa Slough | Marshall, SD | 38.5 miles | NE |
| Dry Lake Number Two | Clark, SD | 44.4 miles | SW |
| Five Ponds | Hamlin, SD | 45.4 miles | SE |
| Slather Slough | Roberts, SD | 46.4 miles | NE |
| Flood Slough | Traverse, MN | 50.1 miles | NE |
| Wet Lake | Traverse, MN | 50.2 miles | NE |
| Conner Slough | Deuel, SD | 55.7 miles | SE |
| Sandy Slough | Big Stone, MN | 57.8 miles | NE |
| Government Slough | Big Stone, MN | 60.4 miles | NE |
| Humpty-dumpty Slough | Big Stone, MN | 61.1 miles | NE |
| Lone Tree Slough | Big Stone, MN | 61.2 miles | NE |
| Sweetwater Lake | Big Stone, MN | 61.3 miles | NE |
| Dismal Swamp | Big Stone, MN | 67.7 miles | NE |
| Griffin Lake | Swift, MN | 75.3 miles | NE |
| Mud Lake | Stevens, MN | 76.8 miles | NE |
| Bracken Slough | Beadle, SD | 77.3 miles | SW |
| Norwegian Slough | Beadle, SD | 77.6 miles | SW |
| Black Slough | Brookings, SD | 77.7 miles | SE |
| Barrows Lake | Grant, MN | 79.9 miles | NE |
| Rifle Lake | Sanborn, SD | 85.4 miles | SW |
| Byrne Lake | Swift, MN | 85.9 miles | NE |
| Coleman Slough | Stevens, MN | 86.1 miles | NE |
| Jones Lake | Grant, MN | 87.7 miles | NE |
| Lanners Lake | Yellow Medicine, MN | 89 miles | SE |
| Tenmile Lake | Lac qui Parle, MN | 89.9 miles | SE |
| Congers Marsh | Yellow Medicine, MN | 90.1 miles | SE |
| Burton Lake | Yellow Medicine, MN | 92.9 miles | SE |
| Burke Slough | Miner, SD | 93.2 miles | SW |
| Reynolds Slough | Lake, SD | 97.3 miles | SE |
| Myhre State Wildlife Management Area | Yellow Medicine, MN | 98.2 miles | SE |
| Schmall Marsh | Grant, MN | 98.3 miles | NE |
| Collins Slough | Hand, SD | 98.7 miles | SW |
| Skogen Marsh | Otter Tail, MN | 99.1 miles | NE |
| Fods Slough | Lake, SD | 99.5 miles | SE |
| Rempfer Lake | Jerauld, SD | 99.6 miles | SW |
| Mahla Lake | Douglas, MN | 102.4 miles | NE |
| Miedd Lake | Yellow Medicine, MN | 102.5 miles | SE |
| Cady Lake | Jerauld, SD | 102.7 miles | SW |
| Lawndale Swamp | Wilkin, MN | 103.8 miles | NE |
| Grow Lake | Jerauld, SD | 108.1 miles | SW |
| Big Slough | Clay, MN | 114.3 miles | NE |
| Iron Lake | Murray, MN | 118.2 miles | SE |
| Clear Lake | Murray, MN | 123 miles | SE |
| Brink Lake | Becker, MN | 134.4 miles | NE |
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