| Name | County or counties | Area | Notes |
| Alder Bottom | Chautauqua | | |
| Allegheny Reservoir | Cattaraugus | | |
| Ashland Flats | Jefferson | | |
| Ausable Marsh | Clinton | | |
| Bashakill | Sullivan | | |
| Baxtertown Woods | Dutchess | | |
| Bear Spring Mountain | Delaware | | |
| Black Pond | Jefferson | | Part of the "Eastern Lake Ontario Barrier Beach and Wetland Complex" New York Natural Heritage Area. |
| Bog Brook | Putnam | | |
| Braddock Bay | Monroe | | |
| Canadaway Creek | Chautauqua | | |
| Canoga Marsh | Seneca | | Protects marshland along the western shore of Cayuga Lake. |
| Capital District | Rensselaer | | |
| Carters Pond | Washington | | |
| Carlton Hill | Wyoming | | |
| Catharine Creek | Schuyler | | |
| Cayuga Lake | Seneca | | |
| Chautauqua Lake | Chautauqua | | |
| Cherry Island | Orange | | Protects an island within the upper Delaware River. |
| Cicero Swamp | Onondaga | | |
| Clay Pond | Chautauqua | | |
| Cold Brook | Steuben | | |
| Collins Landing | Jefferson | | |
| Conesus Inlet | Livingston | | |
| Conewango Swamp | Cattaraugus | | |
| Connecticut Hill | Schuyler, Tompkins | | |
| Cranberry Creek | Jefferson | | |
| Cranberry Mountain | Putnam | | |
| Cross Lake Islands | Cayuga, Onondaga | | |
| Crumhorn Mountain | Otsego | | |
| Currans Road Pond | Suffolk | | |
| Curtiss Gale | Oswego | | |
| Deer Creek Marsh | Oswego | | Part of the "Eastern Lake Ontario Barrier Beach and Wetland Complex" New York Natural Heritage Area. |
| Dexter Marsh | Jefferson | | |
| East Bay | Washington | | |
| Erwin | Steuben | | |
| Fish Creek | St. Lawrence | | |
| Franklinton Vlaie | Schoharie | | |
| French Creek | Jefferson | | |
| Frenchman's Island | Onondaga, Oswego | | Formerly operated as the undeveloped Frenchman Island State Park. Transferred to NYSDEC in 2011, and now part of Three Mile Bay WMA. |
| Galen | Wayne | | |
| Genesee Valley | Allegany | | |
| Great Baehre Swamp | Erie | | |
| Great Swamp | Putnam | | |
| Great Vly | Greene, Ulster | | |
| Hamlin Marsh | Onondaga | | |
| Hampton Brook Woods | Erie | | |
| Hanging Bog | Allegany | | |
| Happy Valley | Oswego | | |
| Hartland Swamp | Niagara | | |
| Hartson Swamp | Chautauqua | | |
| Helmer Creek | Steuben | | |
| High Tor | Ontario, Yates | | |
| Honeoye Creek | Ontario | | |
| Honeoye Inlet | Ontario | | |
| Honeyville | Jefferson | | |
| Hooker Mountain | Otsego | | |
| Indian River | Jefferson | | |
| Jacquins Pond | Chautauqua | | |
| John White | Genesee | | Formerly managed by New York State as the "John White Memorial Game Farm" between 1945 and 2000 for the purpose of raising pheasants for release on public hunting lands. |
| Kabob | Chautauqua | | |
| Keeney Swamp | Allegany | | |
| Kings Bay | Clinton | | |
| Lake Alice | Clinton | | |
| Lake Ontario Islands | Jefferson, St. Lawrence | | Protects the Little Galloo Island, the Gull Island, and a portion of Galloo Island. |
| Lake Shore Marshes | Wayne | | |
| Lakeview | Jefferson | | Part of the "Eastern Lake Ontario Barrier Beach and Wetland Complex" New York Natural Heritage Area. |
| Lewis Preserve | Clinton | | |
| Little John | Oswego | | |
| Louise E. Keir | Albany | | |
| Margaret Burke | Albany | | |
| Mongaup Valley | Sullivan | | |
| Monty's Bay | Clinton | | |
| Motor Island | Erie | | |
| Northern Montezuma | Seneca, Wayne, Cayuga | | |
| Oak Orchard | Genesee | | |
| Oriskany Flats | Oneida | | |
| Otis Pike Preserve | Suffolk | | |
| Parcel 45 | Saratoga | | |
| Partridge Run | Albany | | |
| Pauline Murdock | Essex | | |
| Perch River | Jefferson | | |
| Pharsalia | Chenango | | |
| Plantation Island | Herkimer | | |
| Point Peninsula | Jefferson | | |
| Putts Creek | Essex | | |
| Rattlesnake Hill | Livingston, Allegany | | |
| Roger's Island | Columbia | | |
| Rome | Oneida | | |
| Saratoga Sand Plains | Saratoga | | |
| Silver Lake | Wyoming | | |
| Spicer Creek | Erie | | |
| Stid Hill | Ontario | | |
| Stockport | Columbia | | |
| Three Mile Bay | Oswego | | Incorporates Frenchman's Island. |
| Three Rivers | Onondaga | | |
| Tillman Road | Erie | | |
| Tioughnioga | Madison | | |
| Tivoli Bays | Dutchess | | Designated as a "New York Natural Heritage Area" in 2007. |
| Tonawanda | Genesee, Orleans, Niagara | | |
| Tug Hill | Lewis | | |
| Upper and Lower Lakes | St. Lawrence | | |
| Utica Marsh | Oneida | | |
| Victory Mills | Saratoga | | |
| Vinegar Hill | Greene | | |
| Waneta-Lamoka | Schuyler | | |
| Watt's Flats | Chautauqua | | |
| West Cameron | Steuben | | |
| Whitney Point | Broome, Cortland | | |
| Wickham Marsh | Essex | | |
| Willard | Seneca | | |
| Wilson Hill | St. Lawrence | | |
| Wolf Hollow | Delaware | | |
| Young's Island | Suffolk | | |