| Adams | Bermudian Creek |
| Allegheny | Deer Creek (main stem and tributaries), Pine Creek (tributary to Youghiogheny River), Montour Run, Nine Mile Run, Turtle Creek |
| Armstrong | Crooked Creek (main stem and tributaries) |
| Bedford | Yellow Creek (main stem and tributaries) |
| Berks | Hay Creek, Little Manatawny Creek, Tulpehocken Creek |
| Blair | Clover Creek, Little Juniata River, Sinking Run |
| Bradford | Towanda Creek |
| Bucks | Neshaminy Creek |
| Butler | Connoquenessing Creek (main stem and tributaries) |
| Cambria | Chest Creek (main stem and tributaries), Little Conemaugh River |
| Cameron | Driftwood Branch Sinnemahoning Creek |
| Carbon | Mud Run, Pohopoco Creek |
| Centre | Fishing Creek (main stem and tributaries), Penns Creek (upper and upper-middle sections) |
| Chester | French Creek (tributaries to Schuylkill River), White Clay Creek |
| Clarion | Clarion River (main stem and Toby Creek) |
| Clearfield | Little Clearfield Creek, West Branch Susquehanna River (tributaries in Clearfield County) |
| Clinton | Kettle Creek (middle section) |
| Columbia | Fishing Creek (North Branch and Little Fishing Creek), Roaring Creek (main stem and South Branch) |
| Crawford | Conneaut Outlet |
| Cumberland | Big Spring Creek |
| Dauphin | Armstrong Creek, Clarks Creek, Manada Creek |
| Delaware | Crum Creek, Darby Creek |
| Elk | Little Toby Creek |
| Erie | Elk Creek |
| Fayette | Dunbar Creek, Meadow Run, Redstone Creek |
| Forest | Tionesta Creek |
| Franklin | Conococheague Creek (West Branch and East Branch), Falling Spring Branch |
| Fulton | Big Cove Creek, Licking Creek (main stem and North Branch) |
| Huntingdon | Little Juniata River, Raystown Branch Juniata River (main stem and Kishacoquillas Creek) |
| Indiana | Blacklick Creek, Yellow Creek (South Branch and North Branch) |
| Jefferson | Little Mahoning Creek, Sandy Lick Creek, North Fork Redbank Creek, Piney Creek (Little Toby Creek Division and Sandy Creek Division) |
| Juniata | Honey Creek, Tuscarora Creek |
| Lackawanna | Roaring Brook |
| Lancaster | Mill Creek, Pequea Creek |
| Lawrence | Slippery Rock Creek |
| Lebanon | Quittapahilla Creek |
| Lehigh | Jordan Creek |
| Luzerne | Harveys Creek |
| Lycoming | Lycoming Creek (main stem and Little Pine Creek), Muncy Creek (main stem and Little Muncy Creek), Pine Creek (upper and lower sections) |
| McKean | Marvin Creek, Potato Creek, Kinzua Creek |
| Mercer | Neshannock Creek (main stem and tributaries) |
| Mifflin | Kishacoquillas Creek |
| Monroe | Brodhead Creek, McMichael Creek |
| Montgomery | Valley Creek |
| Montour | Chillisquaque Creek |
| Northampton | Monocacy Creek |
| Northumberland | Chillisquaque Creek, Shamokin Creek |
| Perry | Big Buffalo Creek, Buffalo Creek (main stem and tributaries) |
| Philadelphia | Pennypack Creek |
| Pike | Bushkill Creek |
