| East Vermillion Lake | McCook, SD | 6.1 miles | SE |
| East Fork Vermillion River Reservoir | McCook, SD | 6.1 miles | SE |
| Hanson Lake | Hanson, SD | 25.7 miles | NW |
| Sioux Falls Diversion Channel | Minnehaha, SD | 27.8 miles | NE |
| Swan Lake | Turner, SD | 27.9 miles | SE |
| Lake Fulton | Hanson, SD | 28.9 miles | NW |
| Fulton Lake | Hanson, SD | 29 miles | NW |
| Ethan Lake | Hanson, SD | 32.7 miles | SW |
| Lake Dimock | Hutchinson, SD | 32.7 miles | SW |
| Lake Alvin | Lincoln, SD | 35.9 miles | SE |
| Lake Henry | Bon Homme, SD | 37.3 miles | SW |
| Lake Mitchell | Davison, SD | 38 miles | NW |
| Lake Badus | Lake, SD | 38.5 miles | NE |
| Marindahl Lake | Yankton, SD | 38.7 miles | SE |
| Beaver Lake | Yankton, SD | 41.3 miles | SW |
| Carlson Lake | Lincoln, SD | 41.5 miles | SE |
| Lake Pahoja | Lyon, IA | 43.9 miles | SE |
| Lake Carthage | Miner, SD | 45.1 miles | NW |
| Tripp Lake | Hutchinson, SD | 48 miles | SW |
| Lake Tripp | Hutchinson, SD | 48.1 miles | SW |
| Lake Campbell | Brookings, SD | 48.9 miles | NE |
| Split Rock Lake | Pipestone, MN | 50.7 miles | NE |
| Splitrock Lake | Pipestone, MN | 50.7 miles | NE |
| Lake Yankton | Yankton, SD | 51.5 miles | SW |
| Lewis and Clark Lake | Yankton, SD | 51.7 miles | SW |
| Corsica Lake | Douglas, SD | 52 miles | SW |
| Lake Yankton | Yankton, SD | 52.2 miles | SW |
| Old Stickney Lake | Aurora, SD | 52.2 miles | NW |
| Stickney Lake | Aurora, SD | 53.3 miles | NW |
| Stickney Lake | Aurora, SD | 54.4 miles | NW |
| Rock River Reservoir | Rock, MN | 55 miles | NE |
| North Mound Creek Pool | Rock, MN | 55.8 miles | NE |
| South Mound Creek Pool | Rock, MN | 56.5 miles | NE |
| Steffan Reservoir | Knox, NE | 57.6 miles | SW |
| Bartz Reservoir | Cedar, NE | 57.7 miles | SW |
| Lake Dante | Charles Mix, SD | 57.7 miles | SW |
| Zart Reservoir | Knox, NE | 58.6 miles | SW |
| Lake Iroquois | Kingsbury, SD | 58.6 miles | NW |
| Lake Wagner | Charles Mix, SD | 61.9 miles | SW |
| Shottenkirk Lake | Aurora, SD | 62.6 miles | NW |
| Lake Fraser | Aurora, SD | 63.6 miles | NW |
| Fraser Dam | Aurora, SD | 63.7 miles | NW |
| Lake Agnew | Kingsbury, SD | 65.4 miles | NW |
| Rowan Reservoir | Keya Paha, NE | 65.8 miles | SE |
| Osceola Lake | Kingsbury, SD | 65.8 miles | NW |
| Wilmarth Lake | Aurora, SD | 66.3 miles | NW |
| Stony Run Lake | Beadle, SD | 66.8 miles | NW |
| Laffey Lake | Aurora, SD | 67 miles | SW |
| Aowa Creek Reservoir 61-11A | Dixon, NE | 68.5 miles | SE |
| Vakoc Reservoir | Knox, NE | 68.6 miles | SW |
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