| ID | Basin Name | SWSI |
| 1 | Marias River above Tiber Reservoir | -1.22 |
| 2 | Tobacco River | -1.04 |
| 3 | Kootenai Ft. Steele to Libby Dam | -1.56 |
| 4 | Kootenai River below Libby Dam | -0.91 |
| 5 | Fisher River | -1.74 |
| 6 | Yaak River | -1.25 |
| 7 | North Fk. Flathead River | -0.69 |
| 8 | Middle Fk. Flathead River | -1.39 |
| 9 | South Fk. Flathead River | -0.69 |
| 10 | Flathead River at Columbia Falls | -0.52 |
| 11 | Stillwater/Whitefish | |
| 12 | Swan River | -0.87 |
| 13 | Flathead River at Polson | -1.56 |
| 14 | Mission Valley | |
| 15 | Little Bitterroot River | -1 |
| 16 | Clark Fork River above Milltown | 0.17 |
| 17 | Blackfoot River | -0.69 |
| 18 | Clark Fork River above Missoula | -0.52 |
| 19 | Bitterroot River | -0.52 |
| 20 | Clark Fork River below Bitterroot River | -0.52 |
| 21 | Clark Fork River below Flathead River | -1.1856 |
| 22 | Beaverhead River | 0.17 |
| 23 | Ruby River | -0.69 |
| 24 | Big Hole River | 0.35 |
| 25 | Boulder River (Jefferson) | -1.22 |
| 26 | Jefferson River | 0.21 |
| 27 | Madison River | 0 |
| 28 | Gallatin River | -1.56 |
| 29 | Missouri River above Canyon Ferry | -0.17 |
| 30 | Missouri River below Canyon Ferry | -0.87 |
| 31 | Smith River | -2.27 |
| 32 | Sun River | -1.74 |
| 33 | Teton River | -0.76 |
| 34 | Birch/Dupuyer Creeks | -1.39 |
| 35 | Marias River below Tiber Reservoir | 0.52 |
| 36 | Musselshell River | -1.74 |
| 37 | Missouri River above Fort Peck | -0.6285 |
| 38 | Missouri River below Fort Peck | -0.17 |
| 39 | Milk River | -1.74 |
| 40 | Dearborn River near Craig | -0.83 |
| 41 | Yellowstone River above Livingston | 2.43 |
| 42 | Shields River | -1.04 |
| 43 | Boulder River (Yellowstone) | 0.17 |
| 44 | Stillwater River | 1.04 |
| 45 | Rock/Red Lodge Creeks | 0.87 |
| 46 | Clarks Fork River | 1.74 |
| 47 | Yellowstone River above Bighorn River | 1.7322 |
| 48 | Bighorn River below Bighorn Lake | 2.12271 |
| 49 | Little Bighorn River | 0 |
| 50 | Yellowstone River below Bighorn River | 2.12271 |
| 51 | Tongue River | 1.56 |
| 52 | Powder River | -0.87 |
| 53 | Upper Judith Basin | -3.7 |
| 54 | St. Mary River | -1.22 |