| | Site # | Site Name | Value |
| 29 | FLATHEAD Lake Inflow | 90 |
| 30 | FLINT CREEK blw Boulder Ck | 88 |
| 31 | FLINT CREEK nr Southern | 98 |
| 32 | GALLATIN RIVER at Logan | 68 |
| 33 | GALLATIN RIVER nr Gateway | 77 |
| 34 | GIBSON Reservoir Inflow | 80 |
| 35 | HEBGEN Reservoir Inflow | 74 |
| 36 | HUNGRY HORSE Reservoir | 83 |
| 38 | HYALITE RESERVOIR Inflow | 89 |
| 39 | JEFFERSON RIVER nr Three | 56 |
| 40 | KOOTENAI at Leonia | 98 |
| 42 | LAKE SHERBURNE Inflow | 86 |
| 43 | LIBBY RES Inflow | 99 |
| 45 | LITTLE BIGHORN RIVER nr | 85 |
| 46 | LITTLE BLACKFOOT nr | 71 |
| 47 | LOWER WILLOW CK RES Inflow | 58 |
| 48 | MARIAS RIVER nr Shelby | 78 |
| 49 | MF FLATHEAD nr West Glacier | 89 |
| 50 | MF ROCK CREEK nr | 85 |
| 54 | MISSOURI RIVER at Fort Benton | 69 |
| 55 | MISSOURI RIVER at Toston | 63 |
| 56 | MISSOURI RIVER at Virgelle | 71 |
| 57 | MISSOURI RIVER below Fort | 69 |
| 58 | MISSOURI RIVER nr Landusky | 66 |
| 59 | MUSSELSHELL at Harlowton | 45 |
| 60 | MYSTIC LAKE Reservoir Inflow | 84 |
| 61 | NEVADA CREEK nr Finn | 51 |
| 62 | NF FLATHEAD nr Columbia | 99 |
| 63 | NF MUSSELSHELL nr Delpine | 57 |