Anawalt Lake; Anthony Creek; Big Sandy Creek; Blackwater River; Boley Lake; Brandywine Lake; Brushy Fork Lake; Buckhannon River (railroad); Buffalo Creek (Brooke); Buffalo Creek (Logan); Buffalo Fork Lake; Bullskin Run

Cacapon Park Lake; Castleman Run Lake; Cherry River; Coopers Rock Lake; Cranberry River; Dillons Run; East Fork Greenbrier River; Edwards Run; Elk River; Evitts Run; Fort Ashby Reservoir; French Creek Pond

Gandy Creek; Glade Creek of Mann; Glade Creek of New River; Glady Fork; Greenbrier River; Horseshoe Run; Indian Creek; Kings Creek; Knapps Creek; Laurel Fork (Randolph); Laurel Fork of Holly River; Left Fork of Holly River

Little Kanawha Headwaters; Little River East Fork Greenbrier River; Little River West Fork Greenbrier River; Lost River; Lower Cove Run; Marsh Fork; Middle Creek; Middle Fork; Middle Wheeling Creek Lake; Mill Creek of Opequon Creek; Mill Creek of South Branch; Mill Run of Back Creek

Moores Run; New Creek; North Fork of Anthony Creek; North Fork of Cherry River; North Fork of Patterson Creek; North Fork of South Branch; North River; Opequon Creek; Pinnacle Creek (upper section); Potts Creek; Red Creek; Rich Creek (Monroe)

Right Fork of Little Kanawha Headwaters; Rocky Marsh Run; Seneca Lake; Shavers Fork (Bemis); Shavers Fork (lower); Shavers Fork (upper); South Branch (Franklin); South Branch (Smoke Hole); South Fork of Potts Creek; Spruce Knob Lake; Summersville Tailwaters; Summit Lake

Tilhance Creek; Tuscarora Creek; Tomlinson Run; Trout Run; Tuckhaoe Lake; Tygart Headwaters; Waites Run; Watoga Lake; West Fork Greenbrier River; West Fork Greenbrier River (railroad grade); Williams River