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Allegheny River
  Allegheny River at Salamanca, NY
Angle Fly Brook
Angle Fly Brook at Whitehall Corners, NY
AuSable River
AuSable River near Au Sable Forks, NY
East Branch AuSable River at Au Sable Forks, NY
Batavia Kill
Batavia Kill at Red Falls near Prattsville, NY
Batavia Kill near Maplecrest, NY
Batten Kill
Batten Kill at Battenville, NY
Bear Kill
Bear Kill near Prattsville, NY
Beaver Kill
Beaver Kill at Cooks Falls, NY
Beaver Kill Tributary above Lake Hill, NY
Beaver River
Beaver River at Croghan, NY
Birch Creek
Birch Creek at Big Indian, NY
Biscuit Brook
Biscuit Brook above Pigeon Brook at Frost Valley, NY
Black Creek
Black Creek at Churchville, NY
Black River
Black River at Watertown, NY
Black River near Boonville, NY
Buffalo Creek
Buffalo Creek at Gardenville, NY
Bush Kill
Bush Kill below Maltby Hollow Brook at West Shokan, NY
Bush Kill near Arkville, NY
Callicoon Creek
Callicoon Creek at Callicoon, NY
Canacadea Creek
Canacadea Creek near Hornell, NY
Canandaigua Outlet
Canandaigua Outlet at Chapin, NY
Canaseraga Creek
Canaseraga Creek above Dansville, NY
Canisteo River
Canisteo River at West Cameron, NY
Canisteo River below Canacadea Creek at Hornell, NY
Cattaraugus Creek
Cattaraugus Creek at Gowanda, NY
Cayuga Creek
Cayuga Creek near Lancaster, NY
Cazenovia Creek
Cazenovia Creek at Ebenezer, NY
Chadakoin River
Chadakoin River at Falconer, NY
Chemung River
Chemung River at Chemung, NY
Chemung River at Corning, NY
Chemung River at Elmira, NY
Chenango River
Chenango River at Greene, NY
Chenango River at Sherburne, NY
Chenango River near Chenango Forks, NY
Chestnut Creek
Chestnut Creek at Grahamsville, NY
Cohocton River
Cohocton River at Avoca, NY
Cohocton River at Bath, NY
Cohocton River near Campbell, NY
Coulter Brook
Coulter Brook near Bovina Center, NY
Cross River
Cross River at Katonah, NY
Cross River near Cross River, NY
Croton River
East Branch Croton River at Brewster, NY
East Branch Croton River near Croton Falls, NY
East Branch Croton River near Putnam Lake, NY
Middle Branch Croton River near Carmel, NY
West Branch Croton River at Richardsville, NY
West Branch Croton River near Carmel, NY
West Branch Croton River near Croton Falls, NY
Delaware River
Delaware River above Lackawaxen River near Barryville, NY
Delaware River at Callicoon, NY
Delaware River at Port Jervis, NY
Delaware River near Hankins, NY
East Branch Delaware River at Fishs Eddy, NY
East Branch Delaware River at Harvard, NY
East Branch Delaware River at Margaretville, NY
East Branch Delaware River at Roxbury, NY
West Branch Delaware River at Hale Eddy, NY
West Branch Delaware River at Hancock, NY
West Branch Delaware River at Hobart, NY
West Branch Delaware River at Walton, NY
West Branch Delaware River upstream From Delhi, NY
Dry Brook
Dry Brook at Arkville, NY
East Brook
East Brook East of Walton, NY
East Kill
East Kill near Jewett Center, NY
Ellicott Creek
Ellicott Creek below Williamsville, NY
Esopus Creek
Esopus Creek at Allaben, NY
Esopus Creek at Coldbrook, NY
Fall Creek
Fall Creek near Ithaca, NY
Genesee River
Genesee River at Avon, NY
Genesee River at Ballantyne Bridge near Mortimer, NY
Genesee River at Portageville, NY
Genesee River at Wellsville, NY
Genesee River near Mount Morris, NY
Great Chazy River
Great Chazy River at Perry Mills, NY
Harbor Brook
Harbor Brook at Hiawatha Blvd in Syracuse, NY
Harbor Brook at Syracuse, NY
Hollow Tree Brook
Hollow Tree Brook at Lanesville, NY
Honeoye Creek
Honeoye Creek at Honeoye Falls, NY
Hoosic River
Hoosic River near Eagle Bridge, NY
Hudson River
Hudson River above Lock 1 near Waterford, NY
Hudson River at Albany, NY
Hudson River at Fort Edward, NY
Hudson River at Green Island, NY
Hudson River at Hadley, NY
Hudson River at Lock 1 near Waterford, NY
Hudson River at North Creek, NY
Hudson River at South Dock at West Point, NY
Hudson River at Tomkins Cove, NY
Hudson River below Poughkeepsie, NY
Hudson River near Congers, NY
Hudson River South of Hastings-On-Hudson, NY
Hunter Brook
Hunter Brook South of Yorktown, NY
Independence River
Independence River at Donnattsburg, NY
Kisco River
Kisco River below Mount Kisco, NY
Lake George
Lake George at Rogers Rock, NY
Ley Creek
Ley Creek at Park Street in Syracuse, NY
Little Beaver Kill
Little Beaver Kill at Beechford near Mt Tremper, NY
Little Delaware River
Little Delaware River near Delhi, NY
Mahwah River
Mahwah River near Suffern, NY
Mettawee River
Mettawee River near Middle Granville, NY
Mohawk River
Mohawk River at Cohoes, NY
Mohawk River below Delta Dam near Rome, NY
Mohawk River near Little Falls, NY
Moose River
Moose River at McKeever, NY
Muscoot River
Muscoot River at Baldwin Place, NY
Muscoot River below Dam at Amawalk, NY
Neversink River
Neversink River at Bridgeville, NY
Neversink River near Claryville, NY
Ninemile Creek
Ninemile Creek at Lakeland, NY
Oatka Creek
Oatka Creek at Garbutt, NY
Oatka Creek at Warsaw, NY
Oneida Creek
Oneida Creek at Oneida, NY
Oneida River
Oneida River near Euclid, NY
Onondaga Creek
Onondaga Creek at Dorwin Avenue in Syracuse, NY
Onondaga Creek at Spencer Street in Syracuse, NY
Oswegatchie River
West Branch Oswegatchie River near Harrisville, NY
Oswego River
Oswego River at Lock 7, Oswego, NY
Otselic River
Otselic River at Cincinnatus, NY
Ouleout Creek
Ouleout Creek at East Sidney, NY
Owasco Outlet
Owasco Outlet at Genesee Street Auburn, NY
Owego Creek
Owego Creek near Owego, NY
Platte Kill
Platte Kill at Dunraven, NY
Putnam Creek
Putnam Creek East of Crown Point Center, NY
Ramapo River
Ramapo River at Suffern, NY
Raquette River
Raquette River at Piercefield, NY
Reynolds Channel
Reynolds Channel at Point Lookout, NY
Rondout Creek
Rondout Creek at Rosendale, NY
Rondout Creek near Lowes Corners, NY
Sacandaga River
Sacandaga River at Stewarts Bridge near Hadley, NY
Sacandaga River near Hope, NY
Saranac River
Saranac River at Plattsburgh, NY
Schoharie Creek
Schoharie Creek at Breakabeen, NY
Schoharie Creek at Burtonsville, NY
Schoharie Creek at Prattsville, NY
Schoharie Creek near Lexington, NY
Schroon River
Schroon River at Riverbank, NY
Seneca River
Seneca River (Erie Canal) near Port Byron, NY
Seneca River at Baldwinsville, NY
Sherruck Brook
Sherruck Brook Tributary near Trout Creek, NY
Sixmile Creek
Sixmile Creek at Bethel Grove, NY
St. Regis River
West Branch St. Regis River near Parishville, NY
Stone Hill River
Stone Hill River South of Katonah, NY
Stony Clove Creek
Stony Clove Creek near Phoenicia, NY
Sugarloaf Brook
Sugarloaf Brook South of Tannersville, NY
Susquehanna River
Susquehanna River at Bainbridge, NY
Susquehanna River at Conklin, NY
Susquehanna River at Owego, NY
Susquehanna River at Unadilla, NY
Susquehanna River at Vestal, NY
Susquehanna River at Windsor, NY
Susquehanna River near Waverly, NY
Tioga River
Tioga River at Lindley, NY
Tioga River near Erwins, NY
Tioughnioga River
Tioughnioga River at Cortland, NY
Tioughnioga River at Itaska, NY
Tioughnioga River at Lisle, NY
Titicus River
Titicus River at Purdys Station, NY
Toad Hollow Brook
Toad Hollow Brook near Grand Gorge, NY
Tonawanda Creek
Tonawanda Creek at Batavia, NY
Tonawanda Creek at Rapids, NY
Town Brook
Town Brook Southeast of Hobart, NY
Town Brook Tributary Southeast of Hobart, NY
Trout Creek
Trout Creek near Trout Creek, NY
Tuscarora Creek
Tuscarora Creek above South Addison, NY
Unadilla River
Unadilla River at Rockdale, NY
Wallkill River
Wallkill River at Gardiner, NY
Wappinger Creek
Wappinger Creek near Wappingers Falls, NY
West Canada Creek
West Canada Creek near Wilmurt, NY
West Kill
West Kill below Hunter Brook near Spruceton, NY
West Kill near West Kill, NY
Willow Brook
Willow Bk at College-Staten Island, Staten Island, NY
Wolf Creek
Wolf Creek at Mundale, NY
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