- Anthony Creek
- Bear Rocks Lake
- Big Clear Creek
- Big Sandy Creek
- Blackwater River
- Brandywine Lake
- Brushy Fork Lake
- Buffalo Creek (Logan)
- Buffalo Fork Lake
- Bullskin Run
- Burnsville Tailwaters
- Cacapon Park Lake
- Camp Creek
- Castleman Run Lake
- Cherry River
- Clear Fork of Guyandotte River
- Coopers Rock Lake
- Cranberry River
- Dry Fork (Randolph, Tucker)
- East Fork Greenbrier River
- East River
- Elk River
- Evitts Run
- French Creek Pond
- Gandy Creek
- Glade Creek of Mann
- Glade Creek of New River
- Glady Fork
- Greenbrier River
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- Horseshoe Run
- Kimsey Run Lake
- Knapps Creek
- Laurel Creek of new River
- Laurel Fork (Randolph)
- Laurel Fork of Holly River
- Left Fork of Holly River
- Little Clear Creek
- Little River East Fork Greenbrier River
- Little River West Fork Greenbrier River
- Lost River
- Mash Fork
- Mash Fork of Camp Creek (Children & Class Q)
- Middle Creek
- Middle Wheeling Lake
- Mill Creek of New River
- Mill Creek of Opequon Creek
- New Creek
- North Fork of Anthony Creek
- North Fork of Lunice
- North Fork of Patterson Creek
- North Fork of South Branch
- Opequon Creek
- Pinnacle Creek (lower section)
- Pinnacle Creek (upper section)
- Pond Fork
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- R.D. Bailey Tailwaters
- Red Creek
- Rockcliff Lake
- Rocky Marsh Run
- Seneca Lake
- Shavers Fork (Bemis)
- Shavers Fork (lower section)
- Shavers Fork (upper section)
- South Branch (Franklin)
- South Branch (Smoke Hole)
- South Fork of Cranberry River
- South Mill Creek Lake
- Spruce Knob Lake
- Stonewall Jackson Tailwaters
- Summersville Tailwaters
- Summit Lake
- Sutton Tailwaters
- Teter Creek Lake
- Tilhance Creek
- Trout Run
- Tuscarora Creek
- Tygart Headwaters
- Waites Run
- Warden Lake
- Watoga Lake
- West Fork Greenbrier River
- Wheeling Creek
- Williams River
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