- Anawalt Lake
- Anthony Creek
- Berwind Lake
- Big Clear Creek
- Brandywine Lake
- Brushy Fork Lake
- Bullskin Run
- Cacapon Park Lake
- Cherry River
- Clear Fork of Guyandotte
- Clover Run
- Deer Creek (Nicholas)
- Dillons Run
- Dry Fork (Randolph, Tucker)
- Dry Fork (McDowell)
- Dunloup Creek
- Edwards Run
- Evitts Run
- Fall Run
- Fort Ashby Reservoir
- French Creek Pond
- Gandy Creek
- Hopkins Fork
- Horse Creek Lake
- Jimmy Lewis Lake
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- Kimsey Run Lake
- Knapps Creek
- Laurel Creek of Cherry River
- Left Fork of Holly River
- Little Clear Creek
- Lost River
- Lower Cove Run
- Meadow Creek of Anthony Creek
- Middle Creek
- Mill Creek of Opequon Creek
- Mill Creek of South Branch
- Moores Run
- New Creek
- Newburg Lake
- North Fork of Anthony Creek
- North Fork of Cherry River
- North Fork of Lunice
- North Fork of Patterson Creek
- North Fork of South Branch
- North River
- Opequon Creek
- Paint Creek
- Pinnacle Creek (lower section)
- Pipestem Lake
- Pond Fork
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- Rocky Marsh Run
- Seneca Lake
- Shavers Fork (Bemis)
- Shavers Fork (lower section)
- Shavers Fork (Stuarts Park C&R)
- South Branch (Franklin)
- South Branch (Smoke Hole)
- South Mill Creek Lake
- Teter Creek Lake
- Trout Run
- Tuckahoe Lake
- Tygart Headwaters
- Tygart Tailwaters
- Tuckahoe Lake
- Waites Run
- Wallback Lake
- Warden Lake
- Watoga Lake
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