Tasmania and the Bass Strait islands became separated from mainland Australia around 12,000 BP, when the sea level was about 50 m below present levels. Port Phillip was flooded by post-glacial rising sea levels between 8000 and 6000 years ago.

Oral history and creation stories from the Wada wurrung, Woiwurrung and Bun wurrung languages describe the flooding of the bay. Hobsons Bay was once a kangaroo-hunting