The latter is attributed to combination of the disturbance caused by activity associated with the formerly staffed lighthouse, airstrip, an introduced goat population that was eradicated in 1968, and burrows made by the large numbers of short-tailed shearwaters.

Plant species include sea celery, leek lily, flax lily, coast tussock grass, salt couch, billy button daisies, variable groundsel and an introduced Northern Hemisphere grass, rat's-tail fescue.

Birds of prey include white-bellied sea-eagles, peregrine falcon and swamp harrier with Australian kestrels mainly concentrated on the northern island in the South group.

Other landbirds include white-fronted chats, masked plovers, rock parrots, welcome swallows, silvereyes and stubble quails.

[7] In 1899, it was reported that South Neptune Island "abounded with penguin, and the sandy beach was a favourite resort of the hair seal.

"[13] Another account of the visit said of the muttonbirds: "At night these birds create an indescribable din, in company with the penguins, of which also there is a large number about the various rocks of its coastline.

[10] The islands were first sighted by Europeans on Sunday 21 February 1802 from HMS Investigator whilst under the command of Matthew Flinders.

[19] The islands were subsequently visited by John Lort Stokes in 1840 and later in 1873-74 by Captain F. Howard, RN as part of an ongoing South Australian Government program to map the colony’s waters, identify shipping hazards and assess the suitability of the coastline for settlement.

[7] During World War II, the Neptune Islands became a strategic military site due to its lighthouse’s location at the approaches to both Spencer Gulf and Investigator Strait.

This is evident in the act of the placement of a mine field approximately 25 mi (40 km) west-south west of the Neptune Islands by the German auxiliary cruiser Pinguin during November 1940.

[21] A naval depot including huts and observation towers was established on South Neptune Island along with a gun which was regularly fired.

[26] Located on the largest island in the southern group, a light mounted on a 12-metre-high (39 ft) tower commenced operation in 1983.

[33] The waters around the Neptune Islands outside of the protected area (see below) are commercially fished for abalone, marine scalefish, rock lobster and sardine.

[34][35] Despite their remoteness, the Neptune Islands are regarded as one of South Australia's best scuba diving sites, specifically for the viewing of Great white sharks.

[37][38] Cage diving charters have attracted professional photographers and others whose efforts are considered by individuals such as Rodney Fox as having "significantly contributed to worldwide knowledge of shark physiology and behavior, because film, video, television and print media associated with shark viewing and research activities at the Neptune Islands, have reached a very large global audience".

[34] Other tourist activities include charter fishing, marine mammal watching and cruise ship visits.

[34][47] The keepers' cottages, store, outbuildings, stone fences, stone rainwater tanks, grave sites & footings of the now-removed first lighthouse collectively known as the South Neptune Island Lighthouse Complex are protected under the Heritage Places Act 1993 (SA) and the Development Act 1993 (SA).