- Anthony Creek
- Big Sandy Creek
- Blackwater River
- Boley Lake
- Brandywine Lake
- Brushy Fork Lake
- Buckhannon River
- Buffalo Creek (Brooke)
- Buffalo Fork Lake
- Bullskin Run
- Cacapon Park Lakes
- Castleman Run Lake
- Chief Logan Pond
- Clear Fork of Guyandotte River
- Clear Fork of Guyandotte River (delayed harvest)
- Coopers Rock Lake
- Cranberry River
- Deer Creek (Pocahontas)
- East Fork Greenbrier River
- East River
- Elk River
- Elk River (C&R)
- Evitts Run
- Gandy Creek
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- Glade Creek of Mann
- Glade Creek of New River
- Glady Fork
- Greenbrier River
- Kings Creek
- Knapps Creek
- Laurel Fork (Randolph)
- Left Fork of Right Fork of Buckhannon River
- Little River East Fork Greenbrier River
- Little River West Fork Greenbrier River
- Lost River
- Marsh Fork
- Meadow Creek of New River
- Middle Creek (Berkeley)
- Middle Wheeling Lake
- Mill Creek (Berkeley)
- Moores Run
- New Creek
- North Fork of Patterson
- North Fork South Branch
- Opequon Creek
- Paint Creek
- Panther Creek
- Paw Paw Cree
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- Pinnacle Creek
- Pond fork
- R. D. Bailey Tailwaters
- Right Fork of Buckhannon River
- Rocky Marsh Run
- Shavers Fork (Bemis)
- Shavers Fork (lower section)
- Shavers Fork (upper section)
- South Branch (Franklin)
- South Branch (Smoke Hole)
- South Fork of Cherry River
- South Fork of Cranberry River
- South Mill Creek Lake
- Spruce Knob Lake
- Summit Lake
- Tomlinson Run
- Trout Run
- Tuckahoe Lake
- Waites Run
- Wallback Lake
- Watoga Lake
- West Fork Greenbrier River
- Whiteday Creek
- Williams River
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