| ID | Basin Name | SWSI |
| 1 | Marias River above Tiber Reservoir | -1.4 |
| 2 | Tobacco River | -0.9 |
| 3 | Kootenai Ft. Steele to Libby Dam | -3.1 |
| 4 | Kootenai River below Libby Dam | -1.8 |
| 5 | Fisher River | -1.7 |
| 6 | Yaak River | -1.9 |
| 7 | North Fk. Flathead River | -2.6 |
| 8 | Middle Fk. Flathead River | -3.1 |
| 9 | South Fk. Flathead River | 0.4 |
| 10 | Flathead River at Columbia Falls | -0.2 |
| 11 | Stillwater/Whitefish | |
| 12 | Swan River | -1.2 |
| 13 | Flathead River at Polson | -3.3 |
| 14 | Mission Valley | |
| 15 | Little Bitterroot River | |
| 16 | Clark Fork River above Milltown | -0.9 |
| 17 | Blackfoot River | -1 |
| 18 | Clark Fork River above Missoula | -1.2 |
| 19 | Bitterroot River | -0.7 |
| 20 | Clark Fork River below Bitterroot River | -1.1 |
| 21 | Clark Fork River below Flathead River | -2.5 |
| 22 | Beaverhead River | 0.2 |
| 23 | Ruby River | -0.2 |
| 24 | Big Hole River | -0.2 |
| 25 | Boulder River (Jefferson) | -1 |
| 26 | Jefferson River | 0.2 |
| 27 | Madison River | 0.9 |
| 28 | Gallatin River | -1.4 |
| 29 | Missouri River above Canyon Ferry | -0.5 |
| 30 | Missouri River below Canyon Ferry | -1.2 |
| 31 | Smith River | -1.9 |
| 32 | Sun River | -2.8 |
| 33 | Teton River | -0.4 |
| 34 | Birch/Dupuyer Creeks | -0.9 |
| 35 | Marias River below Tiber Reservoir | 0.2 |
| 36 | Musselshell River | 0 |
| 37 | Missouri River above Fort Peck | -1.1 |
| 38 | Missouri River below Fort Peck | |
| 39 | Milk River | |
| 40 | Dearborn River near Craig | |
| 41 | Yellowstone River above Livingston | 1 |
| 42 | Shields River | -1 |
| 43 | Boulder River (Yellowstone) | -0.5 |
| 44 | Stillwater River | 0.5 |
| 45 | Rock/Red Lodge Creeks | 3 |
| 46 | Clarks Fork River | 2.6 |
| 47 | Yellowstone River above Bighorn River | 1 |
| 48 | Bighorn River below Bighorn Lake | 3.6 |
| 49 | Little Bighorn River | -1.4 |
| 50 | Yellowstone River below Bighorn River | 2.2 |
| 51 | Tongue River | -0.4 |
| 52 | Powder River | -1.7 |
| 53 | Upper Judith Basin | -3.2 |
| 54 | St. Mary River | -2.8 |