| Lake Campbell | Brookings, SD | 18.7 miles | SE |
| Lake Badus | Lake, SD | 25.9 miles | SW |
| Shaokotan Lake | Lincoln, MN | 29.3 miles | SE |
| Canby Lake | Yellow Medicine, MN | 35.8 miles | NE |
| Lake Agnew | Kingsbury, SD | 38.2 miles | NW |
| Osceola Lake | Kingsbury, SD | 43.8 miles | SW |
| Lake Carthage | Miner, SD | 44 miles | SW |
| Lake Iroquois | Kingsbury, SD | 45.4 miles | SW |
| Coon Creek | Lyon, MN | 45.6 miles | SE |
| Staum Dam | Beadle, SD | 47.8 miles | NW |
| Split Rock Lake | Pipestone, MN | 49.8 miles | SE |
| Splitrock Lake | Pipestone, MN | 49.8 miles | SE |
| Brawner Lake | Lyon, MN | 51.1 miles | SE |
| Fordham Dam | Clark, SD | 53 miles | NW |
| Lake Farley | Grant, SD | 53.3 miles | NE |
| Lake Marion | Lyon, MN | 53.3 miles | SE |
| Redwood River Reservoir | Lyon, MN | 55.4 miles | SE |
| Logan Dam | Clark, SD | 55.6 miles | NW |
| Yankton Lake | Lyon, MN | 56.1 miles | SE |
| Dog Creek Reservoir | Lyon, MN | 57.1 miles | SE |
| Mirage Lake | Spink, SD | 60.9 miles | NW |
| Big Stone Lake | Big Stone, MN | 61.3 miles | NE |
| Big Stone Lake-Whetstone River | Lac qui Parle, MN | 61.5 miles | NE |
| Cottonwood Lake | Lyon, MN | 62 miles | NE |
| Sioux Falls Diversion Channel | Minnehaha, SD | 62 miles | SE |
| Sarah Lake | Murray, MN | 62.8 miles | SE |
| Marsh Lake | Swift, MN | 62.9 miles | NE |
| East Fork Vermillion River Reservoir | McCook, SD | 63 miles | SW |
| Ravine Park Lake | Beadle, SD | 63.1 miles | SW |
| East Vermillion Lake | McCook, SD | 63.1 miles | SW |
| Stony Run Lake | Beadle, SD | 63.5 miles | SW |
| Long Tom Lake | Big Stone, MN | 64.1 miles | NE |
| Lac Qui Parle Reservoir | Lac qui Parle, MN | 64.2 miles | NE |
| Lac Qui Parle | Lac qui Parle, MN | 64.2 miles | NE |
| Chippewa River Reservoir | Chippewa, MN | 64.7 miles | NE |
| North Mound Creek Pool | Rock, MN | 64.7 miles | SE |
| South Mound Creek Pool | Rock, MN | 65.2 miles | SE |
| Mill Pond (historical) | Swift, MN | 67 miles | NE |
| Watson Sag | Chippewa, MN | 67.3 miles | NE |
| Shetek Lake | Murray, MN | 68.1 miles | SE |
| Lake Dudley | Spink, SD | 68.2 miles | NW |
| Rock River Reservoir | Rock, MN | 68.4 miles | SE |
| Timm Lake | Yellow Medicine, MN | 69.5 miles | NE |
| Lake Fulton | Hanson, SD | 71.5 miles | SW |
| Fulton Lake | Hanson, SD | 71.6 miles | SW |
| Hanson Lake | Hanson, SD | 73.5 miles | SW |
| Minnesota River Reservoir | Yellow Medicine, MN | 73.6 miles | NE |
| Plum Creek Lake | Redwood, MN | 73.6 miles | SE |
| Lake Alvin | Lincoln, SD | 74 miles | SE |
| Lake Mitchell | Davison, SD | 74.8 miles | SW |
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