| Waterbody |
Region |
| Amawalk Reservoir |
Hudson Valley/Capital District |
| Arthur Kill |
New York City |
| Ashokan Reservoir |
Catskill |
| Atlantic Ocean/Long Island South Shore |
New York City, Long Island (Marine) |
| Beaver Lake |
Adirondack |
| Beaver River |
Adirondack |
| Big Moose Lake |
Adirondack |
| Block Island Sound |
Long Island (Marine) |
| Blue Mountain Lake |
Adirondack |
| Bog Brook Reservoir |
Hudson Valley/Capital District |
| Boyd Corners Reservoir |
Hudson Valley/Capital District |
| Breakneck Pond |
Hudson Valley/Capital District |
| Brown Tract Ponds (Lower and Upper) |
Adirondack |
| Buffalo River and Harbor |
Western |
| Canada Lake |
Adirondack |
| Canadice Lake |
Finger Lakes |
| Cannonsville Reservoir |
Catskill |
| Carry Falls Reservoir |
Adirondack |
| Cayuga Creek |
Western |
| Chase Lake |
Adirondack |
| Chenango River |
Finger Lakes, Leatherstocking/Central |
| Chodikee Lake |
Catskill |
| Cranberry Lake |
Adirondack |
| Crane Pond |
Adirondack |
| Cross River Reservoir |
Hudson Valley/Capital District |
| Dart Lake |
Adirondack |
| Delaware Park Lake/Hoyt Lake |
Western |
| Diverting Reservoir |
Hudson Valley/Capital District |
| Dunham Reservoir |
Hudson Valley/Capital District |
| Dyken Pond |
Hudson Valley/Capital District |
| East Branch Reservoir |
Hudson Valley/Capital District |
| East River |
New York City, Long Island (Marine) |
| East/Middle Stoner Lake |
Adirondack |
| Effley Falls Pond |
Adirondack |
| Eighteenmile Creek |
Western |
| Elmer Falls Pond |
Adirondack |
| Erie Canal |
Western |
| Fall Lake |
Adirondack |
| Ferris Lake |
Adirondack |
| Forked Lake |
Adirondack |
| Fourth Lake of Fulton Chain |
Adirondack |
| Francis Lake |
Adirondack |
| Franklin Falls Flow/Pond |
Adirondack |
| Freeport Reservoir |
Long Island (Freshwater) |
| Fresh Pond (Hither Hills State Park) |
Long Island (Freshwater) |
| Gardiners Bay |
Long Island (Marine) |
| Goodyear Lake |
Leatherstocking/Central |
| Grant Park Pond |
Long Island (Marine) |
| Grass River |
St. Lawrence Valley |
| Great Sacandaga Lake |
Adirondack |
| Halfmoon Lake |
Adirondack |
| Hall's Pond |
Long Island (Freshwater) |
| Harlem River |
New York City |
| Herrick Hollow Creek |
Catskill |
| High Falls Pond |
Adirondack |
| Hinckley Reservoir |
Adirondack, Leatherstocking/Central |
| Hoosic River |
Hudson Valley/Capital District |
| Hudson River |
Hudson River |
| Indian Lake (Town of Diana/Fort Drum) |
Adirondack |
| Indian Lake (Towns of Indian Lake & Lake Pleasant) |
Adirondack |
| Irondequoit Bay |
Finger Lakes |
| Jamaica Bay |
New York City, Long Island (Marine) |
| Keuka Lake |
Finger Lakes |
| Kill Van Kull |
New York City |
| Kinderhook Lake |
Hudson Valley/Capital District |
| Kings Flow |
Adirondack |
| Koppers Pond |
Finger Lakes |
| Lake Capri |
Long Island (Freshwater) |
| Lake Champlain |
Adirondack, St. Lawrence Valley |
| Lake Durant and Rock Pond (Town of Indian Lake) |
Adirondack |
| Lake Eaton |
Adirondack |
| Lake Erie |
Western |
| Lake Ontario |
Finger Lakes, St. Lawrence Valley, Western |
| Lewey Lake |
Adirondack |
| Lewiston Reservoir/Power Reservoir |
Western |
| Limekiln Lake |
Adirondack |
| Lincoln Pond |
Adirondack |
| Loch Sheldrake |
Catskill |
| Lofts Pond |
Long Island (Freshwater) |
| Long Island Sound |
New York City, Long Island (Marine) |
| Long Lake (Town of Long Lake) |
Adirondack |
| Long Pond (Town of Croghan ) |
Adirondack |
| Lower and Upper Sister Lakes |
Adirondack |
| Lower New York Bay |
New York City |
| Lower Saranac Lake |
Adirondack |
| Massapequa Reservoir/Upper Massapequa Reservoir |
Long Island (Freshwater) |
| Massena Power Canal |
St. Lawrence Valley |
| Meacham Lake |
Adirondack |
| Mohawk River |
Leatherstocking/Central |
| Moshier Reservoir |
Adirondack |
| Nassau Lake |
Hudson Valley/Capital District |
| Neversink Reservoir |
Catskill |
| Newark Bay |
New York City |
| Niagara River |
Western |
| North Lake (Town of Ohio) |
Adirondack |
| North-South Lake |
Catskill |
| Onondaga Lake |
Finger Lakes |
| Osgood Pond |
Adirondack |
| Oswego River |
St. Lawrence Valley |
| Peconic Bay |
Long Island (Marine) |
| Pepacton Reservoir |
Catskill |
| Pine Lake |
Adirondack |
| Polliwog Pond |
Adirondack |
| Raquette Lake |
Adirondack |
| Raritan Bay |
New York City |
| Red Lake |
St. Lawrence Valley |
| Ridders Pond |
Long Island (Freshwater) |
| Rio Reservoir |
Catskill, Hudson Valley/Capital District |
| Rollins Pond |
Adirondack |
| Rondout Reservoir |
Catskill |
| Round Pond (Town of Long Lake) |
Adirondack |
| Rushford Lake |
Finger Lakes |
| Russian Lake |
Adirondack |
| Sacandaga Lake |
Adirondack |
| Salmon River |
St. Lawrence Valley |
| Salmon River Reservoir |
St. Lawrence Valley |
| Sand Lake (Town of Arietta) |
Adirondack |
| Sauquoit Creek |
Leatherstocking/Central |
| Saw Mill River |
Hudson Valley/Capital District |
| Schoharie Reservoir |
Catskill |
| Schroon Lake |
Adirondack |
| Seneca River |
Finger Lakes |
| Sheldrake River |
Hudson Valley/Capital District |
| Skaneateles Creek |
Finger Lakes |
| Smith Pond (Rockville Centre) |
Long Island (Freshwater) |
| Smith Pond (Roosevelt Park) |
Long Island (Freshwater) |
| Soft Maple Dam Pond |
Adirondack |
| Soft Maple Reservoir |
Adirondack |
| South Pond (Town of Long Lake) |
Adirondack |
| Spring Lake (Middle Island) |
Long Island (Freshwater) |
| Spy Lake |
Adirondack |
| St. Lawrence River |
St. Lawrence Valley |
| Stark Falls Reservoir |
Adirondack |
| Stillwater Reservoir |
Adirondack |
| Sunday Lake |
Adirondack |
| Susquehanna River |
Finger Lakes |
| Swinging Bridge Reservoir |
Catskill |
| Threemile Creek |
Leatherstocking/Central |
| Titicus Reservoir |
Hudson Valley/Capital District |
| Tupper Lake |
Adirondack |
| Unadilla River |
Leatherstocking/Central |
| Union Falls Flow/Pond |
Adirondack |
| Upper Chateaugay Lake |
Adirondack |
| Upper New York Bay |
New York City |
| Upper Twin Pond |
Long Island (Freshwater) |
| Valatie Kill |
Hudson Valley/Capital District |
| Weller Pond |
Adirondack |
| West Branch Reservoir |
Hudson Valley/Capital District |
| Whitney Park Pond |
Long Island (Freshwater) |
| Willis Lake |
Adirondack |
| Woods Lake |
Adirondack |
