| Five Ponds | Hamlin, SD | 21.8 miles | NW |
| Black Slough | Brookings, SD | 22 miles | NE |
| Wolf Slough | Codington, SD | 29.6 miles | NW |
| Conner Slough | Deuel, SD | 31.4 miles | NE |
| Dry Lake Number Two | Clark, SD | 38.2 miles | NW |
| Fods Slough | Lake, SD | 39.1 miles | SW |
| Reynolds Slough | Lake, SD | 40 miles | SW |
| Caseys Slough | Clark, SD | 43.4 miles | NW |
| Congers Marsh | Yellow Medicine, MN | 43.7 miles | NE |
| Burton Lake | Yellow Medicine, MN | 48.5 miles | NE |
| Dry Lake Number One | Clark, SD | 48.6 miles | NW |
| Lanners Lake | Yellow Medicine, MN | 49.1 miles | NE |
| Burke Slough | Miner, SD | 51.3 miles | SW |
| Myhre State Wildlife Management Area | Yellow Medicine, MN | 57 miles | NE |
| Iron Lake | Murray, MN | 57.5 miles | SE |
| Tenmile Lake | Lac qui Parle, MN | 57.8 miles | NE |
| Rifle Lake | Sanborn, SD | 58.3 miles | SW |
| Miedd Lake | Yellow Medicine, MN | 59.3 miles | NE |
| Mallard Slough | Clark, SD | 60.7 miles | NW |
| Englehardt Slough | Minnehaha, SD | 62.8 miles | SW |
| Clear Lake | Murray, MN | 64.3 miles | SE |
| Forsch Lake | McCook, SD | 65 miles | SW |
| Sandy Slough | Big Stone, MN | 68.5 miles | NE |
| Timm Lake | Yellow Medicine, MN | 69.1 miles | NE |
| Tyson Lake | Yellow Medicine, MN | 69.6 miles | NE |
| Slaughter Slough | Murray, MN | 70.2 miles | SE |
| Griffin Lake | Swift, MN | 71.5 miles | NE |
| Sweetwater Lake | Big Stone, MN | 74.4 miles | NE |
| Humpty-dumpty Slough | Big Stone, MN | 75.5 miles | NE |
| Government Slough | Big Stone, MN | 75.5 miles | NE |
| Dismal Swamp | Big Stone, MN | 75.7 miles | NE |
| Lone Tree Slough | Big Stone, MN | 76.2 miles | NE |
| Norwegian Slough | Beadle, SD | 77.5 miles | SW |
| Wet Lake | Traverse, MN | 78.8 miles | NE |
| Flood Slough | Traverse, MN | 79.4 miles | NE |
| Bracken Slough | Beadle, SD | 81.3 miles | SW |
| Byrne Lake | Swift, MN | 82.4 miles | NE |
| Mud Lake | Stevens, MN | 84.9 miles | NE |
| Willow Lake | Redwood, MN | 86.4 miles | SE |
| Cady Lake | Jerauld, SD | 89.4 miles | SW |
| Coleman Slough | Stevens, MN | 89.8 miles | NE |
| Slather Slough | Roberts, SD | 90.1 miles | NW |
| Wasmund Slough | Osceola, IA | 92.1 miles | SE |
| Grow Lake | Jerauld, SD | 95.7 miles | SW |
| Swan Lake | Cottonwood, MN | 96.9 miles | SE |
| Wilkie Slough | Aurora, SD | 97.5 miles | SW |
| Barrows Lake | Grant, MN | 97.7 miles | NE |
| Rempfer Lake | Jerauld, SD | 98.6 miles | SW |
| Stoa Slough | Marshall, SD | 98.7 miles | NW |
| Plum Lake | Jackson, MN | 100.2 miles | SE |
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