Henderson is one of the last two raised coral atolls in the world whose ecosystems remain relatively unaffected by human contact, along with Aldabra in the Indian Ocean.

Ten of its 51 flowering plants, all four of its land birds and about a third of the identified insects and gastropods are endemic – a remarkable diversity given the island's size.

[3][4] On 29 January 1606, Portuguese captain Pedro Fernandes de Queirós, leading a Spanish expedition in search of the fabled great south land (Terra Australis), was the first European to see the island, and named it San Juan Bautista.

[6] On 20 November 1820, a sperm whale rammed and sank the Nantucket whaleship Essex (a report of which inspired Herman Melville to write Moby-Dick), and the ship's 20 crewmen arrived at Henderson on 20 December in three small whaleboats.

They found the island's only known drinkable water source – a brackish spring on the north shore, exposed at half tide – and ate fish, birds, eggs, crabs and peppergrass, but within a week they had largely exhausted the readily available food.

Therefore, on 27 December, the three boats set sail for South America, leaving behind Thomas Chappel, Seth Weeks and William Wright, who chose to stay and survived until their rescue several months later, on 9 April 1821.

[8] In 1957, a 27-year-old American, Robert Tomarchin, lived the life of a castaway on the island for approximately two months, accompanied by a pet chimpanzee, apparently as a publicity stunt, until people from Pitcairn rescued him in two longboats.

[12] In March 2022 a Royal Navy survey by HMS Spey, as part of an effort to update maritime charts regarding British Overseas Territories, found the island to be 1 nautical mile (1.9 km; 1.2 mi) south of its indicated position.

[13] Since the introduction of aluminium-hulled long-boats in the 20th century, Pitcairners have made regular trips to Henderson to harvest the wood of miro and tou trees.

This coral limestone island sits atop a conical (presumed volcanic) mound, rising from a depth of roughly 3,500 m (11,500 ft).

There is only one known potable water source, a brackish spring on the north shore exposed at half tide, rising from a crevice in flat rock, large surfaces of which compose the face of the beach.

Dominant tree species include coconut palms, Pandanus tectorius, Thespesia populnea (miro), Heliotropium foertherianum, Cordia subcordata (tou), Guettarda speciosa, Pisonia grandis, Geniostoma hendersonense, Nesoluma st-johnianum, Hernandia stokesii, Myrsine hosakae, and Celtis sp.

[16] Between July and November 2011, a partnership of the Pitcairn Islands Government and the Royal Society for the Protection of Birds implemented a poison baiting programme aimed at eradicating the Pacific rat.

[26] Research published in April 2017[27] looked at debris on several beaches, and reported "the highest density of plastic rubbish anywhere in the world" as a result of the South Pacific Gyre.

The study noted that purple hermit crabs (Coenobita spinosus) make their homes in plastic containers washed up on beaches, and the debris may reduce shoreline gastropod diversity, may contribute to a reduction in the number of sea turtle laying attempts and may increase the risk of entanglement for coastal-nesting seabirds.