| Black Slough | Brookings, SD | 21.9 miles | NE |
| Fods Slough | Lake, SD | 29.7 miles | SW |
| Reynolds Slough | Lake, SD | 32.6 miles | SW |
| Five Ponds | Hamlin, SD | 36.5 miles | NW |
| Conner Slough | Deuel, SD | 41.7 miles | NE |
| Congers Marsh | Yellow Medicine, MN | 42.1 miles | NE |
| Wolf Slough | Codington, SD | 44.1 miles | NW |
| Burton Lake | Yellow Medicine, MN | 46.8 miles | NE |
| Iron Lake | Murray, MN | 46.8 miles | SE |
| Lanners Lake | Yellow Medicine, MN | 49.2 miles | NE |
| Burke Slough | Miner, SD | 49.8 miles | SW |
| Dry Lake Number Two | Clark, SD | 50.4 miles | NW |
| Englehardt Slough | Minnehaha, SD | 52.1 miles | SW |
| Clear Lake | Murray, MN | 54.3 miles | SE |
| Myhre State Wildlife Management Area | Yellow Medicine, MN | 55.4 miles | NE |
| Miedd Lake | Yellow Medicine, MN | 56.7 miles | NE |
| Caseys Slough | Clark, SD | 57.4 miles | NW |
| Forsch Lake | McCook, SD | 58.1 miles | SW |
| Slaughter Slough | Murray, MN | 59.4 miles | SE |
| Tenmile Lake | Lac qui Parle, MN | 59.4 miles | NE |
| Rifle Lake | Sanborn, SD | 61 miles | SW |
| Dry Lake Number One | Clark, SD | 62.5 miles | NW |
| Timm Lake | Yellow Medicine, MN | 64.2 miles | NE |
| Tyson Lake | Yellow Medicine, MN | 65.6 miles | NE |
| Mallard Slough | Clark, SD | 74.9 miles | NW |
| Wasmund Slough | Osceola, IA | 77.8 miles | SE |
| Willow Lake | Redwood, MN | 78.5 miles | NE |
| Griffin Lake | Swift, MN | 78.9 miles | NE |
| Sandy Slough | Big Stone, MN | 78.9 miles | NE |
| Sweetwater Lake | Big Stone, MN | 84.6 miles | NE |
| Norwegian Slough | Beadle, SD | 84.7 miles | NW |
| Dismal Swamp | Big Stone, MN | 84.9 miles | NE |
| Humpty-dumpty Slough | Big Stone, MN | 85.8 miles | NE |
| Government Slough | Big Stone, MN | 85.8 miles | NE |
| Swan Lake | Cottonwood, MN | 86.2 miles | SE |
| Lone Tree Slough | Big Stone, MN | 86.5 miles | NE |
| Plum Lake | Jackson, MN | 86.6 miles | SE |
| Sutton Lake Marsh | Osceola, IA | 88.8 miles | SE |
| Byrne Lake | Swift, MN | 88.9 miles | NE |
| Bracken Slough | Beadle, SD | 89 miles | NW |
| Wet Lake | Traverse, MN | 90.8 miles | NE |
| Rush Lake | Jackson, MN | 91.2 miles | SE |
| Flood Slough | Traverse, MN | 91.4 miles | NE |
| Cady Lake | Jerauld, SD | 92.8 miles | SW |
| Mud Lake | Stevens, MN | 93.4 miles | NE |
| Coleman Slough | Stevens, MN | 97.1 miles | NE |
| McBreen Marsh | Dickinson, IA | 98.8 miles | SE |
| Grow Lake | Jerauld, SD | 98.9 miles | SW |
| Wilkie Slough | Aurora, SD | 99 miles | SW |
| Haucks Lake | Bon Homme, SD | 105.6 miles | SW |
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