The New York–New Jersey Harbor Estuary has a variety of flora and fauna. 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 steadily recovering from pollution; ecologically it is true that these waters were once dead or extremely toxic but after 45 years of cleaning the estuary is in a much better state than it has been in a hundred years. Tidal flow occurs as far north as Troy, over 150 miles away. The salt front (dilute salt water) can reach Poughkeepsie in drought conditions and is present in the lower reaches of the Raritan River for most of the year.Hudson Estuary Basics Dept. of Environmental Conservation, NY State.
Animal species
Arthropods American lobster (Homarus americanus) - Massachusetts Bay is not the only home of the lobster on the East Coast. Usually found south of the Verrazzano 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, and just offshore near Ocean County, New Jersey. Depredation by man within the New York-New Jersey Harbor Estuary is extremely rare. Some specimens can be as long as a man's arm. 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) - Also known as the blue claw crab. 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, including the waters just off Coney 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 (Chesapeake Bay) have decreased. Females bearing eggs should be let go immediately because if they are not it affects the next generation. Ghost crab (Ocypode quadrata) - Common sight after twilight scurrying along the beaches of western Long Island and the planktonic larvae are found throughout the estuary. Atlantic horseshoe crab (Limulus polyphemus) - A common visitor to Breezy Point, Rockaways, and Coney Island. Numbers in peril but not yet a candidate as an endangered species. The New York Horseshoe Crab Monitoring Network conducts a citizen science annual census at different sites. Lady crab (Ovalipes ocellatus) Portly spider crab (Libinia emarginata) A species of decorator crab. Like most spider crab It is edible though rarely in the USA on account of appearance. Ivory barnacle (Amphibalanus eburneus) Northern rock barnacle (Semibalanus balanoides) Asian shore crab (Hemigraspus sanguineus) An invasive alien species that is a favorite food of seagulls and other shorebirds in the area. Common Spider Crab (Libinia emarginata) Green Crab (Carcinus maenus) This species is an invasive species originally from Europe that has been present in all waters of the State of New York for many decades. It is a swimmer crab that is present in most parts of the harbor and is easily distinguished from the blue crab by being much smaller and a dull green color. Black fingered mud crab (Panopeus herbstii) Gammarid Amphipod (Family Gammaridae) Corophid amphipod (Family Corophiidae) Skeleton Shrimp (Family Caprellida) Shore Shrimp, Grass Shrimp (Palaemonetes spp.) Sea Roach (Family idoteidae) White fingered mud crab (Rhithropanopeus harrisii)
Chordates
Birds 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) A common sight that is present almost year round. Some will nest on the many tall buildings afforded in all five boroughs, none of which is more than a few miles from the water. American oystercatcher (Haematopus pallatius) American wigeon (Anas americana) Bald eagle (Halieeatus leucocephalus) - Has been seen up the Hudson River every winter consistently for well 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. Will occasionally make itself known in the Lower Harbor seeking schools of mackerel. Black bellied plover (Pluvialis squatarola) Black-crowned night heron (Nycticorax nycticorax) Black skimmer (Rynchops niger) Brant (Branta bernicla hrota) Brown pelican (Pelecanus occidentalis) This bird migrates north from the Chesapeake and Outer Banks in the late spring and does not go back until roughly late September. Occasionally will perch on docks. Prefers alewives and mossbunker; should not be fed so much as a morsel if found on the docks as it can become habituated to humans and an unhealthy diet. Canada goose (Branta canadensis) Glossy ibis (Plegadis falcinellus) A common bird in the summertime in Jamaica Bay and in the shallows on the Pelham Islands. Great blue heron (Ardea herodia) Often found on Staten Island near the water. Green heron (Butorides virescens) Will take to feeding in the Bronx River in summertime. Also found occasionally in Jamaica Bay and marshy portions on the New Jersey side of the estuary, attracted by small fish. Mallard (Anas platyryncha) The most common dabbling duck in the region. A common visitor to brackish portions of the lower Raritan as well as Staten Island. Northern gannet (Morus bassanus) A member of the booby family. Will dive head first into the water after fish. Osprey (Pandion haliaetus) - A very common sight in the skies over western Long Island, especially during the nesting months. Easily seen near Jamaica Bay. Piping plover (Charadrius melodus)-A bird that likes to nest on beaches like the ones near Rockaways and the Pelham Islands. This plover in particular is very tiny and beachgoers must mind their step near sand dunes as they can be missed. Has a pleasant sounding call. Likes to nest on sandy beaches and can be difficult to see during nesting season, as it tries to camouflage itself. This is a very nervous, endangered species that must remain unmolested during nesting as it will abandon its eggs if stressed; birdwatchers are advised to remain very, very quiet and to maintain a long distance from the nest so as not to frighten the bird. Red knot (Calidris canutus rufa) The estuary is a place where the red knot likes to rest as it migrated back to its breeding grounds in the Arctic. Small flocks can be seen in the spring and early summer. This bird's numbers are threatened, and so it must remain undisturbed. Snowy egret (Egretta thula) A common visitor to streams and salt marshes in the summer. Will on rare occasions be found foraging and relaxing in parks and rivers in the estuary system like the Bronx River. Males have very distinct breeding plumage. 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 and ponds in parks.
Fish Alewife (Alosa pseudoharengus) American anglerfish (Lophius americanus) Easily the homeliest fish in the water; Prefers the deepest parts of the estuary and Sandy Hook. Sold in local farmer's markets as monkfish, even though it is not a monkfish in strictu senso. American butterfish (Peprilus triacanthus) American eel (Anguilla rostrata)-Numbers are low; currently on IUCN redlist. Should gently put back exactly where it was found and not bought from any vendor nor taken home to eat anywhere in New York or New Jersey. Will travel thousands of miles to reproduce in Sargasso Sea every year. The Hudson River is a known haunt of this fish as is Upper New York Bay. American shad (Alosa sapidissima) Anadromous fish that once was found as far inland as Bridgewater New Jersey and a former abundant resident of the Raritan River showing signs of returning. American silver perch (Bairdiella chrysoura) Atlantic croaker (Micropogonias undulatus) Atlantic herring (Clupea harengus) Atlantic menhaden (Brevoortia tyrannus)-Also known as mossbunker. This fish is a success story. In the 1940s and 1950s, the waters of the Estuary were very badly polluted and had been polluted since at least the mid 19th century. By the time of the Clean Water Act, the waters surrounding New York City were ecologically dead or dying. As of 2018, however, the water is clean enough to support this fish in obscenely large numbers, which have in turn triggered the return of whales, dolphins, and sharks to the harbor. Atlantic moonfish (Selene setapinnis) Likes to school in large numbers. 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; it also can and does migrate long distances from the mouth of the Hudson. This fish is very large as an adult and can grow to 14 feet long. It should be put back at once if caught on a line and the state environmental authorities should be contacted, with a photograph if possible. The Atlantic sturgeon is an endangered fish that has been the victim of overfishing for caviar as well as the alteration of its habitat in too many rivers along the East Coast. The Hudson River and the New York-New Jersey Harbor Estuary is a clear nursery for this fish as well as a stronghold for the species overall: the most recent research suggests that the remaining populations in other rivers in other states are interconnected with New York's, evidenced by tracking devices. Other populations in Europe were, at one point, completely wiped out. Banded killifish (Fundulus diaphanus) Bay anchovy (Anchoa mitchilli) Black drum (Pogonias cromis) Black seabass (Centropristis striata) Blueback herring (Alosa aestivalis) Bluefish (Pomatomus saltatrix) Cunner (Tautogolabrus adspersus) Crevalle jack (Caranx hippos) Foureye butterflyfish (Chaetodon capistratus) Fourspot flounder (Hippoglossina oblonga) Gizzard shad (Dorosoma cepedianum) Hogchoker (Trinectes maculatus) Lined seahorse (Hippocampus erectus) Found all over the harbor and Sandy Hook. A species that should be gently put back exactly where it was found if caught, or as close to seagrass as possible. Numbers are threatened by collectors seeking Traditional Chinese Medicine. Should not be purchased at all from such vendors. Mummichog (Fundulus heteroclitus) Northern pipefish (Syngnathus fuscus) Northern sea robin (Prionotus carolinus)