- Anthony Creek
- Back Fork of Elk River
- Big Clear Creek
- Big Sandy Creek
- Blackwater River
- Boley Lake
- Brandywine Lake
- Brushy Fork Lake
- Buckhannon River
- Buffalo Creek (Brooke)
- Buffalo Fork Lake
- Bullskin Run
- Burnsville Tailwaters
- Cacapon Park Lake
- Castleman Run Lake
- Cherry River
- Clear Fork of Guyandotte River
- Coopers Rock Lake
- Cranberry River
- Desert Fork
- Dillons Run
- Dry Fork (Randolph, Tucker)
- East Fork Greenbrier River
- Edwards Run
- Elk River
- Evitts Run
- Fort Ashby Reservoir
- Gandy Creek
- Glade Creek of Mann
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- Glade Creek of New River
- Glady Fork
- Greenbrier River
- Indian Rocks Lake
- Kimsey Run Lake
- 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
- Middle Creek
- Middle Fork River
- Middle Wheeling Lake
- Mill Creek of Opequon Creek
- Mill Creek of South Branch
- New Creek
- North Fork of Cherry River
- North Fork of Patterson Creek
- North River
- North Fork South Branch
- Opequon Creek
- Paint Creek
- Paw Paw Creek
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- Pinnacle Creek (lower section)
- Pond Fork
- R.D. Bailey Tailwaters
- Right Fork of Middle Fork River
- Rockcliff Lake
- 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
- Spruce Knob Lake
- Stonewall Jackson Tailwaters
- Sugar Creek
- Summersville Tailwaters
- Summit Lake
- Sutton Tailwaters
- Teter Creek Lake
- Tygart Headwaters
- Trout Run
- Waites Run
- Warden Lake
- Watoga Lake
- West Fork Greenbrier River
- Whiteday Creek
- Williams River
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