| Unknown |
| Abets Creek |
| Acabonack Harbor |
| Agawam Lake |
| Amityville Creek |
| Aspatuck Creek and River |
| Atlantic Ocean |
| Awixa Creek |
| Beaverdam Creek |
| Beaverdam Pond |
| Bellport Bay |
| Belmont Lake |
| Big Reed Pond |
| Big/Little Fresh Ponds |
| Block Island Sound |
| Brightwaters Canal |
| Brown Creek |
| Brushes Creek |
| Carlls River |
| Carmans River Lower, and Tribs |
| Carmans River Upper, and Tribs |
| Centerport Harbor |
| Champlin Creek |
| Cold Spring Harbor, and Tidal Tribs |
| Cold Spring Pond and Tribs |
| Connetquot River, Lower, and Tribs |
| Connetquot River, Upper, and Tribs |
| Conscience Bay and Tidal Tribs |
| Corey Lake and Creek, and Tribs |
| Crab Meadow Creek |
| Deep Pond |
| Duck Island Harbor |
| Dunton Lake, Upper, and Tribs |
| Far Pond |
| Fish Cove |
| Flanders Bay, East/Center, and Tribs |
| Flanders Bay, West/Lower Sawmill Creek |
| Flax Pond |
| Forge River Cove and Tidal Tribs |
| Forge River and Tidal Tribs |
| Fort Pond |
| Fort Pond Bay |
| Fresh Pond |
| Fresh Pond Creek and Tribs |
| Gardiners Bay and minor Tidal Tribs |
| Georgica Pond |
| Goose Neck Creek |
| Grand Canal |
| Great Cove |
| Great Peconic Bay and minor coves |
| Great South Bay, East |
| Great South Bay, Middle |
| Great South Bay, West |
| Green Creek, Upper, and Tribs |
| Halsey Neck Pond |
| Harts Cove |
| Heady and Taylor Creeks and Tribs |
| Hog Creek and Tidal Tribs |
| Hook Pond |
| Howell's Creek |
| Huntington Bay |
| Huntington Harbor |
| Kellis Pond |
| Lake Montauk |
| Lake Panamoka (Long Pond) |
| Lake Ronkonkoma |
| Lawrence Creek/Lakes, O-co-nee |
| Ligonee Brook and Tribs |
| Little Long, and Shorts Pond |
| Little Peconic Bay |
| Little Sebonac Creek |
| Lloyd Harbor |
| Long Island Sound, Suffolk Co, Central |
| Long Island Sound, Suffolk County, West |
| Mecox Bay and Tribs |
| Meetinghouse Creek and Tribs |
| Middle Pond |
| Mill Creek and Tidal Tribs |
| Mill Pond and Sevens Ponds |
| Moriches Bay East |
| Moriches Bay West |
| Mt Sinai Harbor and Tidal Tribs |
| Mud Creek, Robinson Pond, and Tribs |
| Mud and Senix Creeks |
| Napeague Bay |
| Napeague Harbor and Tidal Tribs |
| Narrow Bay |
| Neguntatogue Creek |
| Nicoll Bay |
| Nissequogue River Lower |
| Nissequogue River Upper |
| North Sea Harbor and Tribs |
| Northport Bay |
| Northport Harbor |
| Northwest Creek and Tidal Tribs |
| Northwest Harbor |
| Noyack Bay |
| Noyack Creek and Tidal Tribs |
| Ogden Pond |
| Old Fort Pond |
| Old Town Pond |
| Orchard Neck Creek |
| Oyster Pond/Lake Munchogue |
| Pardees, Orowoc Lakes, Creek, & Tribs |
| Patchogue Bay |
| Patchogue River |
| Pattersquash Creek |
| Peconic River Middle, and Tribs |
| Peconic River Upper, and Tribs |
| Peconic River, Lower, and Tidal Tribs |
| Penataquit Creek |
| Penniman Creek and Tidal Tribs |
| Penny Pond and Creeks |
| Phillips Creek, Lower, and Tidal Tribs |
| Port Jefferson Harbor, North, and Tribs |
| Port Jefferson Harbor, South, and Tribs |
| Quantuck Bay |
| Quantuck Canal/Moneybogue Bay |
| Quantuck Creek and Old Ice Pond |
| Quogue Canal |
| Red Creek Pond and Tidal Tribs |
| Reeves Bay and Tidal Tribs |
| Sag Harbor |
| Sag Harbor Cove and Tribs |
| Sagaponack Pond |
| Sampawams Creek |
| Sans Souci Lakes |
| Santapogue Creek |
| Scallop Pond |
| Seatuck Cove and Tidal Tribs |
| Sebonac Cr/Bullhead Bay and Tidal Tribs |
| Setauket Harbor |
| Sheepen Creek |
| Shelter Island Sound South |
| Shinnecock Bay Central |
| Shinnecock Bay East |
| Shinnecock Bay West |
| Smithtown Bay |
| Speonk River |
| Stillman Creek |
| Stony Brook Harbor |
| Swan River, Swan Lake, and Tidal Tribs |
| Terrell River |
| Terry's Creek and Tribs |
| Three Mile Harbor |
| Tiana Bay and Tidal Tribs |
| Tuthill Cove |
| Tuthills Creek |
| Unchachogue/Johns Neck Creeks |
| Wading River |
| Wainscott Pond/Fairfield Pond |
| Weesuck Creek and Tidal Tribs |
| Wickapogue Pond |
| Wildwood Lake (Great Pond) |
| Willets Creek |
| Wooley Pond |