The reef complex is named after the whaling ship Chesterfield, commanded by Matthew Bowes Alt, which sailed through the Coral Sea in the 1790s.

A barrier reef surrounds the lagoon, interrupted by wide passes except on its eastern side where it is open for over 20 nautical miles (37 km).

[3] He had delivered convicts to New South Wales in 1793 and was on his way to China to pick up a cargo at Canton to take back to Britain for the British East India Company when he passed the reefs in February–March 1793.

Lieutenant John Lamb, R.N., Commander of the ship Baring, spent three days in the neighborhood of Booby and Bellona Shoals and reefs.

In May 1859 Henry Mangles Denham found Long Island was "a heap of 'foraminifera' densely covered with stunted bush‑trees with leaves as large as cabbage plants, spreading 12 feet (3.7 m) and reaching as high, upon trunks 9 inches (23 cm) diameter...

"[citation needed] Although wooded in the 1850s, it was stripped during guano extraction in the 1870s and was said to be covered in grass with only two coconut trees and some ruins at the south end early in the 20th century.

Terry Walker reported that by 1990 there was a ring of low Tournefortia trees growing around the margin, herbs, grass and shrubs in the interior, and still a few exotic species including coconuts.

The Avon Isles are described by Denham in 1859 as "densely covered with stunted trees and creeping plants and grass, and... crowded with the like species of birds.

The reefs to the south were found next by Mathew Boyd in the convict ship Bellona on his way from Sydney to Canton (modern day Guangzhou) in February or March 1793.

The reefs continued to present a hazard to shipping plying between Australia and Canton or India (where cargo was collected on the way home to Europe).

Denham's conclusions are engraved on British Admiralty Chart 349:These Plans and a mast‑head Lookout will enable a Ship to round to under the lee of the Reefs where she may caulk topsides, set up rigging, rate Chronometers, [and] obtain turtle, fish and seafowl eggs.

Denham, and for the sake of castaways, cocoa‑nuts, shrubs, grasses & every description of seed likely to grow, were sown in the way to promote the superstructure; and it is most desirable that these Refuge‑ spots should be held sacred for universal benefit and not ruthlessly destroyed by the Guano‑seeker.

L. Thiercelin reported that in July 1863 the islets only had two or three plants, including a bush 3–4 m high, and were frequented by turtles weighing 60 to 100 kg.

[13] A collection of birds said to have been made by Surgeon Jourde of the French whaler Général d’Hautpoul on the Brampton Shoals in July 1861 was subsequently brought by Gerard Krefft (1862) to the Australian Museum, but clearly not all the specimens came from there.

When in 1877 Joshua William North also found guano on the Chesterfield Reefs, Alcide Jean Desmazures persuaded Governor Orly of New Caledonia to send the warship La Seudre to annex them.

[citation needed] Apparently the islands were then abandoned until Commander Arzur in the French warship Dumont d’Urville surveyed the Chesterfield Reefs and erected a plaque in 1939.

[14] It revealed, among other things, a variety of avian parasites including a widespread Ornithodoros tick belonging to a genus carrying arboviruses capable of causing illness in humans.