- Lower - from the Camas Prairie Railroad Bridge at Lewiston upstream to the Cherrylane Bridge.
- Middle - from the Cherrylane Bridge upstream to the Orofino Bridge, excluding the perimeter of Dworshak National Fish Hatchery at Ahsahka, and excluding the ladder to the Nez Perce Tribal Hatchery as marked by posted boundaries about 100 yards upstream and downstream of the ladder and extending into the river about 50 yards.
- Upper - from the Orofino Bridge upstream to the South Fork Clearwater River.
- Pine Bar - From the Rice Creek Bridge upstream to the posted boundary about 200 yards downstream of the Hammer Creek boat ramp.
- Hammer Creek - From a posted boundary about 200 yards downstream from the Hammer Creek boat ramp upstream to the U.S. Highway 95 Time Zone Bridge.
- Park Hole - From the Time Zone Bridge upstream to a posted boundary at the mouth of Short's Creek, about 1.4 miles upstream of the mouth of the Little Salmon River.
- Lower - From the mouth to a posted boundary about 200 yards upstream of the mouth of the Rapid River.
- Upper - from the posted boundary about 200 yards upstream of the Rapid River upstream to the U.S. Highway 95 Bridge near Smokey Boulder Road.
- Vinegar Creek - From posted boundary at the mouth of Shorts' Creek upstream to the uppermost boat ramp at Vinegar Creek.