The South Neptune Islands sit on a shelf 70 kilometres south-south east from Port Lincoln, in South Australia. The depth of water on the eastern side of the islands is 40 metres deep dropping steeply to over 95 metres on the southern and western side of the islands. The group named South Neptune Islands consists of two islands forming a rough crescent broken in half by a channel running from the south west to the north east. A large headland, which supports a major fur seal colony, sits west of the southern island, separated by a small channel approximately 4 metres wide.

The islands are comprised of hard and brittle grey granite with a grey coastal loam covering the sheltered areas of the two islands. The southern island, which supports the lighthouse and cottage, slopes moderately from the northeast to the southwest to a high point of 37 metres upon which stands the lighthouse. The lighthouse island covers 104 hectares. The northern island has raised headlands with a plateau wobbling from the south west in a slight rise up to 35 metres, running north east. The northern island covers 98 hectares.