| 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 |