N.Y. Comp. Codes R. & Regs. tit. 9, § 384.17
| Alder Lake | Ulster |
| Allegany River | Cattaraugus |
| Allen Lake | Allegany |
| Alma Pond | Allegany |
| Balsam Pond | Chenango |
| Basher Kill Marsh | Sullivan |
| Bear Lake | Chautauqua |
| Bear Swamp Pond | Otsego |
| Black Creek | Monroe |
| Black Pond | Franklin |
| Black River (x3) | Lewis |
| Black River (Turin) | Lewis |
| Bog River Flow | St. Lawrence |
| Brant Lake | Warren |
| Brown Tract Pond | Hamilton |
| Buffalo River (x2) | Erie |
| Butterfield Lake | Jefferson |
| Canadice Lake | Ontario |
| Canandaigua Lake (x2) | Ontario |
| Canandaigua Lake (Outlet) | Ontario |
| Carmans River/Shirley | Suffolk |
| Caroga Lake | Fulton |
| Carters Pond | Washington |
| Cascade Lakes (Upper and Lower) | Essex |
| Case Lake | Cattaraugus |
| Cassadaga Lake | Chautauqua |
| Cattaraugus Creek | Cattaraugus |
| Cayuga Lake | Cayuga |
| Cayuta Lake | Schuyler |
| Chautauqua Lake (Bemus Point) | Chautauqua |
| Chautauqua Lake (Prendergast Point) | Chautauqua |
| Chazy Lake | Clinton |
| Chemung River (Botchers Landing) | Chemung |
| Chemung River (Dunn Field Stadium) | Chemung |
| Chemung River (Elmira) | Chemung |
| Chemung River (Botchers Landing) | Chemung |
| Chemung River (Golden Glo) | Chemung |
| Chemung River (Minier Park) | Chemung |
| Chemung River (Toll Bridge Park) | Chemung |
| Chemung River (Corning) | Steuben |
| Chemung River | Steuben |
| Chemung River (Greene) | Chenango |
| Chemung River (Halfway House) | Chenango |
| Chemung River (Norwich) | Chenango |
| Chemung River (Sherburne) | Chenango |
| Chittning Pond | Oneida |
| Chodikee Lake | Ulster |
| Clear Pond | Lewis |
| Cleveland Lake | Lewis |
| Cliff Lake | Sullivan |
| Colwell Pond | Jefferson |
| Conesus Inlet | Livingston |
| Conesus Lake (Pebble Beach) | Livingston |
| Conesus Lake (Sand Point) | Livingston |
| Cossayuna Lake | Washington |
| Cranberry Lake | St. Lawrence |
| Crusoe Creek | Wayne |
| Crystal Lake | Sullivan |
| Cuba Lake | Allegany |
| Deep Pond/Riverhead | Suffolk |
| Delaware River (East Branch) | Delaware |
| Delaware River (Hancock) | Delaware |
| Delaware River (West Branch x2) | Delaware |
| Delaware River (Sparrowbush) | Orange |
| Delaware River (Callicoon) | Sullivan |
| Delaware River (Highland) | Sullivan |
| Delaware River (Narrowsburg) | Sullivan |
| Delaware River (Skinners Falls) | Sullivan |
| Dryden Lake | Tompkins |
| Eagle Lake | Essex |
| East Pine Pond | Franklin |
| Eaton Brook Reservoir | Madison |
| Eighth Lake | Hamilton |
| Findley Lake | Chautauqua |
| Fish Creek (West Branch) | Oneida |
| Follensby Clear Pond | Franklin |
| Forestport Reservoir | Oneida |
| Forge Pond (Peconic River)/ Calverton | Suffolk |
| Forked Lake | Hamilton |
| Fort Pond/East Hampton | Suffolk |
| Fourth Lake | Hamilton |
| Francis Lake | Lewis |
| Franklin Falls Flow | Essex |
| Genesee River (Avon) | Livingston |
| Genesee River | Monroe |
| Genesee River (Brown's Bridge) | Monroe |
| Goodyear Lake | Otsego |
| Grass Lake | St. Lawrence |
| Grass River | St. Lawrence |
| Great Sacandaga Lake (Broadalbin) | Fulton |
| Great Sacandaga Lake (Northhampton) | Fulton |
| Great Sacandaga Lake (Northville) | Fulton |
| Great Sacandaga Lake | Saratoga |
| Greens Lake | Greene |
| Guilford Lake | Chenango |
| Guyanoga Creek | Yates |
| Harwood Lake | Cattaraugus |
| Hemlock Lake (Livonia) | Livingston |
| Hemlock Lake (Canadice) | Ontario |
| Honeoye Creek | Monroe |
| Hoosic River/Buskirk | Rensselaer |
| Horseshoe Lake | St. Lawrence |
| Hudson River (Bethlehem) | Albany |
| Hudson River (Coeymans) | Albany |
| Hudson River (Germantown) | Columbia |
| Hudson River (Tivoli Bays) | Dutchess |
| Hudson River (Ulster-Charles Rider Park) | Ulster |
| Hudson River | Warren |
| Hyde Lake | Jefferson |
| Indian Lake | Hamilton |
| Indian River | Jefferson |
| Indian River (Rossie) | St. Lawrence |
| Kinderhook Lake | Columbia |
| Lake Bonaparte | Lewis |
| Lake Colby | Franklin |
| Lake Champlain | Clinton |
| Lake Champlain (Crown Point Reservation) | Essex |
| Lake Champlain (Port Douglas) | Essex |
| Lake Champlain (Port Henry) | Essex |
| Lake Champlain (Ticonderoga) | Essex |
| Lake Champlain (Westport) | Essex |
| Lake Champlain (Willsboro Bay) | Essex |
| Lake Champlain (South Bay) | Washington |
| Lake Erie (Hanover) | Chautauqua |
| Lake Flower | Franklin |
| Lake George (Mossy Point) | Essex |
| Lake George (Northwest Bay Brook) | Warren |
| Lake George (Million Dollar Beach) | Warren |
| Lake Huntington | Sullivan |
| Lake-of-the-Woods | Jefferson |
| Lake Ontario (Black River Bay, Lloyds Landing) | Jefferson |
| Lake Ontario (Black River Bay, Muskellunge Crk.) | Jefferson |
| Lake Ontario (Lyme) | Jefferson |
| Lake Ontario (Perch River) | Jefferson |
| Lake Ontario (Sandy Creek) | Monroe |
| Lake Ontario (Slater Creek) | Monroe |
| Lake Ontario (East Bay x2) | Wayne |
| Lake Ontario (Port Bay South) | Wayne |
| Lake Ontario (Port Bay West) | Wayne |
| Lake Ozonia | St. Lawrence |
| Lake Placid | Essex |
| Lake Ronkonkoma/Islip | Suffolk |
| Lake Superior | Sullivan |
| Lakeview Pond | Jefferson |
| Lamoka Lake | Schuyler |
| Laurel Lake/Southold | Suffolk |
| Lebanon Reservoir | Madison |
| Lime Lake | Cattaraugus |
| Little Clear Pond | Franklin |
| Little Green Pond | Franklin |
| Little Long Lake | Oneida |
| Little Pond | Delaware |
| Long Island Sound/Mattituck Creek | Suffolk |
| Long Island Sound | Suffolk |
| Long Lake | Hamilton |
| Long Pond (x2) | Chenango and Lewis |
| Long Pond | Chenango |
| Lower Yaphank Lake/Yaphank | Suffolk |
| Madison Reservoir | Madison |
| Millsite Lake | Jefferson |
| Mirror Lake | Essex |
| Mohawk River/Barge Canal (Frankfort) | Herkimer |
| Mohawk River/Barge Canal (Herkimer) | Herkimer |
| Mohawk River/Barge Canal (Little Falls) | Herkimer |
| Mohawk River/Barge Canal (Mohawk) | Herkimer |
| Mohawk River/Barge Canal (Amsterdam x2) | Montgomery |
| Mohawk River/Barge Canal (Canajoharie) | Montgomery |
| Mohawk River/Barge Canal (Nelliston) | Montgomery |
| Mohawk River/Barge Canal (Rome) | Oneida |
| Mohawk River/Barge Canal (Utica x3) | Oneida |
| Mohawk River/Barge Canal | Schenectady |
| Mongaup Falls Reservoir | Sullivan |
| Mongaup Pond | Sullivan |
| Moon Lake | Jefferson |
| Moose Pond | Essex |
| Moshier Reservoir | Herkimer |
| Nanticoke Lake | Broome |
| New Albion Lake | Cattaraugus |
| Nicks Lake | Herkimer |
| North Lake | Greene |
| Oatka Creek | Monroe |
| Olean Creek | Cattaraugus |
| Oneida Lake | Madison |
| Oneida Lake (Godfrey Point) | Oneida |
| Oneida Lake (Toad Harbor) | Oswego |
| Oneida River | Onondaga |
| Onteora Lake | Ulster |
| Oswegatchie River (West Branch) | Lewis |
| Oswegatchie River (Edwards x2) | St. Lawrence |
| Oswegatchie River | St. Lawrence |
| Oswegatchie River (Antwerp) | Jefferson |
| Otis Pike Presesrve/Calverton | Suffolk |
| Otisco Lake | Onondaga |
| Otselic River (x2) | Cortland |
| Oyster Bay Harbor | Nassau |
| Papish Pond | Cortland |
| Payne Lake (x2) | Jefferson and Lewis |
| Payne Lake | Jefferson |
| Peconic River (Lower)/Riverhead | Suffolk |
| Peconic River (Upper)/Calverton | Suffolk |
| Portaferry Lake | St. Lawrence |
| Roundout Creek | Ulster |
| Rio Reservoir | Sullivan |
| Queechy Lake | Columbia |
| Quiver Pond | Herkimer |
| Racquette Lake | Hamilton |
| Racquette River | Franklin |
| Red Lake | Jefferson |
| Rock Pond | Lewis |
| Salmon River Reservoir | Oswego |
| Salmon River Reservoir (Little America) | Oswego |
| Salmon River Reservoir (Redfield x2) | Oswego |
| Sangerfield River | Chenango |
| Santa Clara Flow | Franklin |
| Saranac Lake (Lower) | Franklin |
| Saranac Lake (Middle) | Franklin |
| Saranac Lake (Upper/Indian Carry) | Franklin |
| Saranac Lake (Upper/Saranac Inn) | Franklin |
| Schoharie Creek (x2) | Montgomery and Schoharie |
| Schoharie Creek (Central Bridge) | Schoharie |
| Schroon Lake | Essex |
| Seneca River (x2) | Cayuga and Seneca |
| Seneca River (Port Byron) | Cayuga |
| Seneca Lake | Yates |
| Seventh Lake | Hamilton |
| Sixberry Lake | Jefferson |
| Sixtown Pond | Jefferson |
| Sixtown Pond (Crystal Lake) | Jefferson |
| Skaneateles Lake | Onondaga |
| Soft Maple Reservoir | Lewis |
| South Lake | Herkimer |
| South Sandy Creek | Jefferson |
| Spruce Pond | Onondaga |
| St. Regis River | St. Lawrence |
| Star Lake | St. Lawrence |
| Stillwater Reservoir | Herkimer |
| Sucker Lake | St. Lawrence |
| Susquehanna River (Johnson City) | Broome |
| Susquehanna River (Nineveh) | Broome |
| Susquehanna River (Afton) | Chenango |
| Susquehanna River (Otego) | Delaware |
| Susquehanna River (Unadilla) | Delaware |
| Susquehanna River (Colliersville) | Otsego |
| Susquehanna River (Crumhorn) | Otsego |
| Susquehanna River (Emmons) | Otsego |
| Susquehanna River (Oneonta) | Otsego |
| Susquehanna River (Sidney) | Otsego |
| Susquehanna River (Apalachin) | Tioga |
| Susquehanna River (Barton) | Tioga |
| Susquehanna River (Nichols East) | Tioga |
| Susquehanna River (Nichols West) | Tioga |
| Susquehanna River (Oswego) | Tioga |
| Sylvia Lake | St. Lawrence |
| Taylor Pond | Clinton |
| Thompsons Lake | Albany |
| Tioughnioga River (Chenango Forks) | Broome |
| Tioughnioga River (Itasca) | Broome |
| Trout Pond | Lewis |
| Tully Lake | Cortland |
| Tupper Lake | Franklin |
| Twitchell Lake | Herkimer |
| Unadilla River (Guilford) | Chenango |
| Unadilla River (South New Berlin x2) | Chenango |
| Upper Chateaugay Lake | Clinton |
| Upper Leland Pond | Madison |
| Wallkill River | Ulster |
| Walton Lake | Orange |
| Waneta Lake | Schuyler |
| Weaver Lake | Herkimer |
| West Lake | Fulton |
| West River | Yates |
| White Lake | Sullivan |
| White Pond | Putnam |
| Whitney Point Reservoir (Dorchester Park) | Broome |
| Whitney Point Reservoir (Triangle) | Broome |
| Wildwood Lake/Southampton | Suffolk |
| Yellow Lake | St. Lawrence |