Interference with the vegetation of the eastern cay occurred as a result of phosphate mining and secondly during the period when the Australian Military Forces used the area as a bombing target.

The Capricorn and Bunker Cays form part of a distinct geomorphic province at the southern end of the Great Barrier Reef (Hopley 1982).

The sea level was much lower during the last Ice Age (at the end of the Pleistocene period) and the coastal plain on which today's reefs and cays developed was completely exposed.

Fairfax Islands area a Closed Ring Reefs and the two coral cays belong to two distinct types:[3] In 1803 Captain Eber Bunker of the whaling ship Albion 1798 whaler (2) was the first European to discover the region and gave his name to the southern group.

[4] Albion was 362 tons and registered in London,[5] the ship was fitted with 10 guns, and had a crew of 26; she was built in Deptford, Britain, and owned by, Messrs. Champion; and used for general cargo.

[6] The southern cays and reefs were first chartered between 1819 and 1821 by Royal Navy Lieutenant Phillip Parker King initially aboard Mermaid and later in Bathurst.

The steamer Lady Musgrave, which was chartered by the company for this work, returned to Bundaberg on Sunday afternoon, bringing Mr. A. E. Ellis, the local manager, and account forty Japanese, whose services are being dispensed with.

So bad was the weather, that in fourteen days the vessel was only able to Steam for fifty hours, the steamer having to take shelter behind one of the islands from the heavy squalls and rain.

Heavy weather was encountered, and at 3 p.m. on Sunday the line parted, and notwithstanding all the efforts made, it proved impossible to pick up the ketch again, and it was decided to make for Burnett Heads, which were not reached, as stated, till 4 p.m. the same day.

"[9]Yet when the Queensland government ichthyologist, Mr T. C. Marshall, visited Fairfax Island shortly after 1945, he commented that the gannet rookery there "was not one tenth its pre-war size when you could hardly move among the thousands of nests without stepping upon one of them", and he attributed the decline of the bird population to naval bombing practices during the war.

[10] Another report in 1953 by C. Roff, described the effects of bombing practice at Fairfax Island as having "Large [breeding] numbers of the brown gannet" (Sula leucogaster).

[14] Diana, a wooden carvel schooner / brig of 103 tons and 70 feet (21 m) in length built in Sydney in 1847 by the builder Ale and owned by C.L.