The Bunurong Aboriginal people lived around Western Port for tens of thousands of years, enjoying a range of shellfish, mutton birds and plantlife.

In 1797, George Bass received permission from Governor Hunter in Sydney to sail a whaleboat along the unexplored section of coast south of Botany Bay. On such a rough stretch of water, Bass could not get more than halfway through the strait now known as Bass Strait. This voyage led to the discovery of Western Port, so named because of its situation relative to every other known harbour on the coast at that time.

In the early 19th century, the bay played a role in the struggle between Britain and France. Soldiers and convicts from Sydney were ordered to form a camp at Western Port to deter possible occupation by the French. It was only after the end of World War 2 that serious consideration was given to the development of the Bay as a port, and its flat shores north of Stony and Crib Points have become a centre for heavy industry.