| Peg Munky Run | Brookings, SD | 3.9 miles | NE |
| Bullhead Run | Hamlin, SD | 6.3 miles | NE |
| Hidewood Creek | Hamlin, SD | 7.4 miles | NW |
| Sixmile Creek | Brookings, SD | 14 miles | SE |
| Stray Horse Creek | Hamlin, SD | 14.5 miles | NW |
| North Deer Creek | Brookings, SD | 15 miles | SE |
| Dolph Creek | Hamlin, SD | 15.7 miles | NW |
| Lake Campbell Outlet | Brookings, SD | 19.1 miles | SE |
| Deer Creek | Brookings, SD | 19.2 miles | SE |
| Battle Creek | Moody, SD | 20.6 miles | SE |
| Deer Creek | Brookings, SD | 21.5 miles | SE |
| Medary Creek | Lincoln, MN | 22.1 miles | SE |
| Medary Creek | Lincoln, SD | 22.1 miles | SE |
| Medary Creek | Moody, MN | 22.1 miles | SE |
| Medary Creek | Moody, SD | 22.1 miles | SE |
| North Branch Cobb Creek | Deuel, SD | 27.3 miles | NE |
| Willow Creek | Codington, SD | 27.5 miles | NW |
| Cobb Creek | Deuel, MN | 30 miles | NE |
| Cobb Creek | Deuel, SD | 30 miles | NE |
| Cobb Creek | Yellow Medicine, MN | 30.1 miles | NE |
| Cobb Creek | Yellow Medicine, SD | 30.1 miles | NE |
| Spring Creek | Lincoln, MN | 30.7 miles | SE |
| Spring Creek | Lincoln, SD | 30.7 miles | SE |
| Spring Creek | Moody, MN | 30.7 miles | SE |
| Spring Creek | Moody, SD | 30.7 miles | SE |
| Mud Creek | Moody, SD | 33.6 miles | SE |
| Monighan Creek | Deuel, MN | 33.9 miles | NE |
| Monighan Creek | Deuel, SD | 33.9 miles | NE |
| Monighan Creek | Lac qui Parle, MN | 33.9 miles | NE |
| Monighan Creek | Lac qui Parle, SD | 33.9 miles | NE |
| Mud Creek | Codington, SD | 34 miles | NW |
| Silver Creek | Lake, SD | 34.6 miles | SW |
| Flandreau Creek | Moody, MN | 35 miles | SE |
| Flandreau Creek | Moody, SD | 35 miles | SE |
| Flandreau Creek | Pipestone, MN | 35 miles | SE |
| Flandreau Creek | Pipestone, SD | 35 miles | SE |
| Norwegian Creek | Lincoln, MN | 35.9 miles | SE |
| Park Creek | Lake, SD | 36.1 miles | SW |
| Willow Creek | Pipestone, MN | 36.4 miles | SE |
| East Branch Flandreau Creek | Pipestone, MN | 36.6 miles | SE |
| Caine Creek | Deuel, SD | 36.7 miles | NE |
| Squaw Creek | Moody, SD | 37.1 miles | SE |
| Crow Timber Creek | Deuel, SD | 39 miles | NE |
| Negro Creek | Lake, SD | 39.4 miles | SW |
| Canby Creek | Yellow Medicine, MN | 39.7 miles | NE |
| Crow Creek | Deuel, MN | 40.3 miles | NE |
| Crow Creek | Deuel, SD | 40.3 miles | NE |
| Wolf Drain | Lake, SD | 40.3 miles | SW |
| Mahoney Creek | Codington, SD | 40.5 miles | NW |
| North Buffalo Creek | Lake, SD | 40.6 miles | SW |
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