The marine life of New York–New Jersey Harbor Estuary refers to the variety of flora and fauna in and around Port of New York and New Jersey. For bodies of water within the estuary see Geography of New York-New Jersey Harbor Estuary. Much of the harbor originally consisted of tidal marshes that have been dramatically transformed by the development of port facilities. The estuary itself supports a great variety of thriving estuarine aquatic species; contrary to popular stereotypes, New York Harbor and its adjacent, interdependent waters are very much alive, and recovering from pollution. Tidal flow occurs as far north as Troy, over 150 miles away. The salt front (dilute salt water) can reach Poughkeepsie in drought conditions.
American lobster (Homarus americanus) - Massachusetts Bay is not the only home of the lobster on the East Coast. Usually found south of the Verrazano Bridge, near the Southwestern end of Long Island and just off Sandy Hook. Often attracted to artificial reefs found near Lower New York Bay, where they can reach very large sizes. Depredation by man within the New York-New Jersey Harbor Estuary is extremely rare.
Atlantic rock crab (Cancer irroratus) - A common crab found on the continental shelf within ten miles of shoreline. Found in all parts of the estuary. There is some concern over it competing with the invasive European green crab for habitat, but it is believed that the presence of Callinectes genera in the bight may offer some refuge as it has been shown that the swimmer crabs of this genus like to prey upon the smaller green crab.
Blue crab (Callinectes sapidus) - The crabs are typically found in the mouth of the Hudson River and occasionally wander into the brackish waters of small rivers and coves that pepper the western side of Long Island; up the Hudson they are found occasionally in the part of the river that runs through the lower Hudson Valley in the summertime. Up until the 1960s they could be eaten, but the State of New York currently recommends against attempting to do so on a regular basis, due to bioaccumulation of PCBs and cadmium that were discovered in the crabs in the 1970s. On the upside, a lack of hunting by man has caused this crab's numbers to grow heartily while others (notably the Chesapeake Bay) have decreased.
Ghost crab (Ocypode quadrata) - Common sight after twilight scurrying along the beaches of western Long Island and the planktonic larvae is found all throughout the estuary.
Atlantic horseshoe crab (Limulus polyphemus) - A common visitor to Breezy Point, Rockaways, and Coney Island.
Lady crab (Ovalipes ocellatus)
Portly spider crab (Libinia emarginata)
Although not aquatic animals, these birds are supported by the food and habitat the harbor provides, particularly Jamaica Bay and the Pelham Islands. Many of these birds will fly within sight of the Manhattan skyline and the estuary is a very important point for the East Coast because of its location: it is dead center in the Atlantic Flyway and many raptors and waterfowl use this spot as a rest area along their journey from New England and Canada in fall before heading further south to the Southern States and the Caribbean, reversing the journey in late March and early April.
American herring gull (Larus smithsonianus)
Black-crowned night heron (Nycticorax nycticorax)
Great blue heron (Ardea herodia)
Snowy egret (Egretta thula)
Yellow-crowned night heron (Nycticorax violaceus) - Nests on some of the uninhabited islands in the harbor and feasts upon the fish in the ocean and frogs in the streams
American oystercatcher (Haematopus pallatius)
American wigeon (Anas americana)
Bald eagle (Halieeatus leucocephalus) - Has been seen up the Hudson River every winter consistently for over a decade, feeding on a wide variety of both freshwater and saltwater fish. Has also been seen using the New Jersey Palisades and piers near the Harlem River as a perch from which to swoop down and grab its quarry in the estuary.
Black skimmer (Rynchops niger)
Brant (Branta bernicla hrota)
Canada goose (Branta canadensis)
Great white heron - Adults spotted since 2009. In late May 2012 there have been numerous juveniles spotted.
Mallard (Anas platyryncha)
Osprey (Pandion haliaetus) - A very common sight in the skies over western Long Island, especially during the nesting months.
Alewife (Alosa pseudoharengus)
American butterfish (Peprilus triacanthus)
American eel (Anguilla rostrata)
American shad (Alosa sapidissima)
Atlantic herring (Clupea harengus)
Atlantic menhaden (Brevoortia tyrannus)
Atlantic needlefish (Strongylura marina)
Atlantic silverside (Menidia menidia)
Atlantic sturgeon (Acipenser oxyrinchus) - Found in the depths of Upper New York Bay, in the main channel of the Hudson River
Black drum (Pogonias cromis)
Bluefish (Pomatomus saltatrix)
Gizzard shad (Dorosoma cepedianum)
Lined seahorse (Hippocampus erectus)
Mummichog (Fundulus heteroclitus)
Northern pipefish (Syngnathus fuscus)
Sand lance (Ammodytes americanus)
Scup (Stenatomus chrysops)
Striped bass (Morone saxatilis) - One of the most prevalent species in the harbor, and the most extensively fished one. The Hudson River Estuary system has been a nursery for stripers going back before European settlement and overall it is one of the most important breeding grounds for this species in the Northeast.
Summer flounder (Paralicthys dentatus)
Tautog (Tautoga onitis)
Tomcod (Microgadus tomcod)
Weakfish (Cynoscion regalis)
White perch (Morone americana)
Winter flounder (Pleuronectes americanus)
Bottlenose dolphin (Tursiops truncatus)
Grey seal (Halichoerus gryphus)
Harbor seal (Phoca vitulina) - Historically both pinniped species were abundant natives in the harbor until hunting and other human activity extirpated them from the area by at least the late 19th century. In recent years, however, these two species, along with the some more typically northerly seal species like the harp seal have been found in the harbor in pursuit of some of the species mentioned above. Colonies of harbor seals can be found happily basking in the sun off Staten Island and Jamaica Bay from December through April, and as of 2011 they have been spotted playing just off Coney Island.
Harbor porpoise (Phocoena phocoena) - Has been seen in Upper New York Bay.
North American river otter (Lutra canadensis) - Native to the Hudson River and occasionally is seen at the mouth of the river. Restoration efforts by the state of New York are underway and appear to be successful.
Whales
Blue whale (Balaenoptera musculus)
Fin whale (Balaenoptera physalus)
Humpback whale (Megaptera novaeangliae)
Minke whale (Balaenoptera acutorostrata)
North Atlantic right whale (Eubalaena glacialis)
From 2007-2009, an expert from Cornell University did an experiment listening in on the acoustics of the Harbor Estuary, where, to the astonishment of many, he discovered at least six species of whale vocalizing less than 20 miles from where the Statue of Liberty stands, just past the Verrazano Bridge where the water gets deeper. Historical records show that whales were plentiful in the area going well back into colonial history: in 1697, the charter for Trinity Church received its official royal charter, which gave it not only a large chunk of land in Lower Manhattan, but also the profit from any whales or shipwrecks along the banks of the Hudson. The return of these whales is evidence of environment's improvement over the past thirty years: in 2009, a young humpback whale attempted to penetrate the gateway to the upper harbor when it passed under the Verrazano Bridge, causing the men and women ashore watching the whole debacle from Fort Hamilton a great deal of concern for its health and the safety of the Coast Guard officers trying to herd it back out to sea (the whale returned unharmed.)
White cross hydromedusa (Staurophora mertensi)
Atlantic starfish (Asterias forbesi)
Northern sea star (Asterias vulgaris)
Atlantic bay scallop (Aequipectin irradians)
Atlantic jackknife clam (Ensis directus)
Atlantic surf clam (Spisula solidissima)
Blue mussel (Mytulis edulis)
Eastern oyster (Crassostrea virginica) - Once widely found through much of the harbor and a staple of the local diet from the time of the Algonquians up through the 19th century. Oystering grounds were prevalent in the Upper Bay, as well as along the south shore of Staten Island and Jamaica Bay. The oyster still exists in the harbor but is not yet considered edible; there are plans to further clean up the areas so that the beds can be restored.
Quahog (Venus mercenaria)
Steamer clam (Mya arenaria)
Longfin inshore squid (Loligo pealei) - Found in Lower New York Harbor and Sheepshead Bay. Often for sale in local farmers' markets.
Channeled whelk (Busycon canaliculatum)
Common periwinkle (Littorina littorea) - Almost certainly introduced in colonial times by the British as food and possibly in bilgewater from ships. Common sight clinging to rocks or wherever their favorite algae can grow.
