| Stream | |
| Klamath River Basin | |
| Jenny Creek | |
| Applegate River Sub-Basin | |
| Little Applegate River | |
| Waters Creek | |
| Ninemile Creek | |
| Star Gulch | |
| Cow Creek Sub-Basin | |
| Starvout Creek | |
| Snow Creek | |
| Riffle Creek | |
| Whitehorse Creek | |
| West Fork Cow Creek | |
| Cow Creek below Dad's Creek | |
| Rattlesnake Creek | |
| Rogue River Tributaries | |
| Grave Creek | |
| West Fork Evans Creek | |
| East Fork Evans Creek | |
| North Fork Big Butte Creek | |
| South Fork Big Butte Creek | |
| Big Butte Creek above Clark Creek | |
| Beaverdam/Vine Maple Creek | |
| Elk Creek | |
| Pickett Creek | |
| Galice Creek | |
| South Fork Little Butte Creek above Lost Creek | |
| Illinois River Sub-Basin | |
| North Fork Deer Creek | |
| South Fork Deer Creek | |
| Crooks Creek | |
| Upper Althouse Creek | |
| Upper Sucker Creek | |