| Sixmile Creek | Brookings, SD | 3.1 miles | SW |
| North Deer Creek | Brookings, SD | 3.4 miles | SW |
| Deer Creek | Brookings, SD | 4.5 miles | SE |
| Lake Campbell Outlet | Brookings, SD | 5.5 miles | SW |
| Medary Creek | Moody, MN | 7.9 miles | SE |
| Medary Creek | Moody, SD | 7.9 miles | SE |
| Medary Creek | Lincoln, MN | 7.9 miles | SE |
| Medary Creek | Lincoln, SD | 7.9 miles | SE |
| Battle Creek | Moody, SD | 8.5 miles | SW |
| Spring Creek | Lincoln, MN | 16 miles | SE |
| Spring Creek | Lincoln, SD | 16 miles | SE |
| Spring Creek | Moody, MN | 16 miles | SE |
| Spring Creek | Moody, SD | 16 miles | SE |
| Peg Munky Run | Brookings, SD | 16.1 miles | NW |
| Deer Creek | Brookings, SD | 18.6 miles | NE |
| Mud Creek | Moody, SD | 19 miles | SE |
| Flandreau Creek | Moody, MN | 20.3 miles | SE |
| Flandreau Creek | Moody, SD | 20.3 miles | SE |
| Bullhead Run | Hamlin, SD | 20.3 miles | NW |
| Flandreau Creek | Pipestone, MN | 20.3 miles | SE |
| Flandreau Creek | Pipestone, SD | 20.3 miles | SE |
| Hidewood Creek | Hamlin, SD | 21.6 miles | NW |
| Willow Creek | Pipestone, MN | 22.5 miles | SE |
| Squaw Creek | Moody, SD | 22.6 miles | SE |
| East Branch Flandreau Creek | Pipestone, MN | 23.9 miles | SE |
| Norwegian Creek | Lincoln, MN | 26 miles | SE |
| Silver Creek | Lake, SD | 26 miles | SW |
| Bachelor Creek | Moody, SD | 26.4 miles | SE |
| Park Creek | Lake, SD | 26.6 miles | SW |
| North Branch Pipestone Creek | Pipestone, MN | 27.7 miles | SE |
| South Branch Pipestone Creek | Pipestone, MN | 28.2 miles | SE |
| Negro Creek | Lake, SD | 28.5 miles | SW |
| Stray Horse Creek | Hamlin, SD | 29 miles | NW |
| Dolph Creek | Hamlin, SD | 29.3 miles | NW |
| Brookfield Creek | Moody, SD | 29.3 miles | SE |
| North Buffalo Creek | Lake, SD | 29.4 miles | SW |
| Wolf Drain | Lake, SD | 29.7 miles | SW |
| Buffalo Creek | Lake, SD | 29.7 miles | SW |
| North Branch Cobb Creek | Deuel, SD | 33.4 miles | NE |
| Cobb Creek | Deuel, MN | 34.7 miles | NE |
| Cobb Creek | Deuel, SD | 34.7 miles | NE |
| Cobb Creek | Yellow Medicine, MN | 34.8 miles | NE |
| Cobb Creek | Yellow Medicine, SD | 34.8 miles | NE |
| East Branch Rock River | Pipestone, MN | 37.5 miles | SE |
| Pipestone Creek | Pipestone, MN | 38.4 miles | SE |
| Pipestone Creek | Pipestone, SD | 38.4 miles | SE |
| Pipestone Creek | Minnehaha, MN | 38.4 miles | SE |
| Pipestone Creek | Minnehaha, SD | 38.4 miles | SE |
| Monighan Creek | Deuel, MN | 40.2 miles | NE |
| Monighan Creek | Deuel, SD | 40.2 miles | NE |
|