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.
 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.
 Despite popular belief, sharks are perfectly capable of living in  the waters of the estuary as well as the deeper waters near Sandy Hook. This would include the very small species to the giants, with 25 of them being recorded as indigenous to the waters of New York State in total. They were once fairly common to the estuary, as evidenced by records left behind by the Dutch describing them in a way that is unmistakable for any other family of fish, and cousins of sharks like the skates and rays never totally went extinct in the waters off New York or New Jersey. Among the rays and sharks, there are many nomadic species that migrate.
 The overwhelming majority of sharks have no interest in hunting humans, as there is plenty of prey available for them to hunt in the nearby waters. Larger species of shark prefer seals, dolphins, and large fish like tuna and billfish, which are found in the waters around the estuary. Most shark species are not known to prey on humans, with increased attacks occurring when natural prey is scarce. The New York Bight, the triangle of water with Montauk at one apex, the Jersey Shore at the second apex, and New York Harbor in the middle, is known for its abundance of marine life, thus providing a large amount of prey for sharks. The exact migration pattern is not completely known and currently being studied, but the general belief is that the larger pelagic sharks migrate north in the spring and return again to Florida and Georgia by the end of November as the water becomes too cold to be bearable. The waters in this area are also a haven for the larger species[citation needed] whose numbers are threatened as shark finning is forbidden by the State of New York.
 Rays
 Cownose ray (Rhinoptera bonasus)
 All marine mammals are protected under the Marine Mammals Protection Act of 1972.
 Whales
 All whales that visit the estuary are wild animals; many, like the humpback, may be mothers with calves.  The water from their blowholes will usually be visible long before the rest of the body is. They will defend themselves vigorously and violently if they believe they or their babies are in danger. A recommended distance of at least 100 yards must be maintained between a vessel and the whale, and pursuing one when it does not seek contact is illegal. It is not unknown for some species to be inquisitive and should the whale approach willingly, the boatmen must turn off the engine and give the beast a way out so that if the whale feels uneasy, it can leave.
 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 the environment's improvement over the past forty years: whales have been absent from New York's waters west of the Hamptons for over a hundred years as the water became incredibly polluted and in 1989 the population was zero.  In 2009, however, 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 alarm, concerned for its health and the safety of the Coast Guard officers trying to herd the frightened, massive creature back out to sea (the whale returned unharmed.)  In late 2017, for the first time, Woods Hole Oceanographic Institute in partnership with the New York Aquarium began to count the whales in a census as the population has expanded mightily.