The St Vincent basin is formed from Cenozoic sediments deposited over, and surrounded by, Proterozoic and Paleozoic rock.

[5] Around 55 million years ago Gondwanaland broke up and Australia separated from Antarctica, causing a number of basins to form along the southern Australian coastline.

Around 40 million years ago a number of blocks formed with the Mount Lofty Ranges rising to the east of the St Vincent basin.

Its entrances from the southwest are from Investigator Strait, and to the southeast from Backstairs Passage, which separate Kangaroo Island from the mainland.

The Aboriginal name given to it by the original inhabitants of the area, the Kaurna people was Wongajerla,[7] also spelt Wongga Yerlo[8] or Wonggayerlo, meaning "western sea".