| Portneuf Dam | Caribou, ID | 9.9 miles | NW |
| Twentyfour Mile Dam | Caribou, ID | 11.1 miles | NE |
| Soda Dam | Caribou, ID | 11.8 miles | SE |
| Alexander Dam | Caribou, ID | 11.8 miles | SE |
| Last Chance Dam | Caribou, ID | 13.1 miles | SE |
| Grace Dam | Caribou, ID | 13.3 miles | SE |
| Soda Creek Dam | Caribou, ID | 14.7 miles | SE |
| Cove Dam | Caribou, ID | 15.3 miles | SE |
| China Cap Dam | Caribou, ID | 16 miles | NE |
| Beker Tailings Number Three Dam | Caribou, ID | 17 miles | SE |
| Conda Site Tailings Dam | Caribou, ID | 17.9 miles | SE |
| Blackfoot Dam | Caribou, ID | 20.1 miles | NE |
| Simplot Number Six Tailings Dam | Caribou, ID | 20.8 miles | SE |
| Wiregrass Dam | Bannock, ID | 24.2 miles | SW |
| Unit Three Haulroad Dam | Caribou, ID | 24.7 miles | NE |
| Enders Dam | Caribou, ID | 26 miles | NE |
| Grays Lake Dam | Caribou, ID | 26.6 miles | NE |
| Stewart Ranch Dam | Caribou, ID | 26.7 miles | SE |
| Hawkins Dam | Bannock, ID | 27.8 miles | SW |
| Current Creek Dam | Bannock, ID | 28.4 miles | SE |
| Stock Valley Dam | Franklin, ID | 28.6 miles | SE |
| Andreason Number Three Dam | Franklin, ID | 29.6 miles | SE |
| Little Valley Dam | Bonneville, ID | 30.5 miles | NE |
| Fife Dam | Bear Lake, ID | 30.7 miles | SE |
| Simplot Effluent Irrigation Dam | Bannock, ID | 30.9 miles | NW |
| Red Pine Canyon Dam | Bear Lake, ID | 31.2 miles | SE |
| Oxford Dam | Franklin, ID | 32.4 miles | SW |
| Oneida Dam | Franklin, ID | 33 miles | SE |
| Grays Lake Dam | Bonneville, ID | 33.2 miles | NE |
| Casperson Dam | Franklin, ID | 34.5 miles | SE |
| Strongarm Reservoir Number One Dam | Franklin, ID | 35.2 miles | SE |
| Devil Creek Dam | Oneida, ID | 35.3 miles | SW |
| Welling Number Two Dam | Bear Lake, ID | 35.5 miles | SE |
| Blackfoot-Equalizing Dam | Bingham, ID | 35.9 miles | NW |
| Strongarm Reservoir Number Two Dam | Franklin, ID | 36.3 miles | SW |
| Condie Dam | Franklin, ID | 36.9 miles | SE |
| Twin Lakes Northwest Dam | Franklin, ID | 37.8 miles | SW |
| Winder Dam | Franklin, ID | 38.7 miles | SE |
| Twin Lakes Southwest Dam | Franklin, ID | 38.7 miles | SW |
| Deep Creek Dam | Oneida, ID | 39.5 miles | SW |
| Daniels Dam | Oneida, ID | 39.5 miles | SW |
| Hammond Dam | Bear Lake, ID | 39.7 miles | SE |
| Upper Deep Creek Dam | Oneida, ID | 40.2 miles | SW |
| Elkhorn Dam | Oneida, ID | 40.3 miles | SW |
| Saint John Dam | Oneida, ID | 41.1 miles | SW |
| Birch Creek Dam | Bonneville, ID | 41.4 miles | NE |
| Crowther Dam | Oneida, ID | 41.7 miles | SW |
| Bohn Dam | Bonneville, ID | 42.1 miles | NE |
| Glendale Dam | Franklin, ID | 42.7 miles | SE |
| Foster Dam | Franklin, ID | 42.8 miles | SE |
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