Flinders navigated inland from the present location of Port Augusta to within 44–39 km (27–24 mi) of the termination of the water body.

[3] By the 1830s, the natural harbour of Port Lincoln had become the site of an unofficial settlement, due in part to its convenience as a base for whaling vessels – which had long operated in the Great Australian Bight.

[2] At the time of Flinders' exploration the gulf was noted to extend 298 km (185 mi) inland from a point near the Port Augusta crossing.

[1] This so-called extension of the gulf consists of a land depression and occasional watercourse known as the Pirie–Torrens corridor, and the inland waterbody Lake Torrens.

The rocky inshore reef along the coast near Port Bonython and Point Lowly is a breeding ground for the Northern Spencer Gulf population of Australian giant cuttlefish.

[4][5][6] They are a favorite food of local bottlenose dolphins, who have developed sophisticated techniques for safely eating these creatures.

A relic population of tiger pipefish (Filicampus tigris), a subtropical species is range limited to Northern Spencer Gulf.

[10] New Zealand fur seals and Australian sea lions can be found in southern Spencer Gulf, with significant breeding colonies located at Dangerous Reef and in the Sir Joseph Banks Group.

They are: The Spencer Gulf region, its wildlife and its development are the subjects of a documentary film in production (as of 2020) entitled Cuttlefish Country.

Blanche Harbour-Douglas Bank Aquatic Reserve which is located in west side of Spencer Gulf, north of Whyalla, was declared in 1980 'for fisheries management, protection of its mangrove-seagrass communities and associated fish nursery areas.

'[35][36] Goose Island Aquatic Reserve which is located at Goose Island on the east side of Spencer Gulf near Port Victoria was d eclared in 1971 to provide 'a conservation area where teaching institutions may conduct classes and scientific research on marine biology and ecology and to protect the habitat of the seal colony situated on White Rocks.

Fishing is prohibited with Sanctuary Zones, and detailed maps and GPS coordinates for the parks are available from the Government of South Australia's Department of Environment, Water & Natural Resources.