The remains of shellfish and other animals are found in large numbers in shell middens at numerous sites adjacent to the marine national park. These remains are evidence that the Indigenous people used the marine environment as a source of food.

In early European settlement, Port Phillip Heads was the major access point to the grazing lands of the early colony and later to the rich goldfields of central Victoria. As a consequence a vast number of ships from other parts of the world plied their way through Port Philip Heads, some of which came to grief on the hidden reefs and the narrow entrance to the Bay. A number of the wrecks that occurred in this area are now found within the Port Phillip Heads Marine National Park. These include the Holyhead, George Roper and Conside on the Lonsdale Reef.
The Eliza Ramsden near Point Nepean and the William Salthouse, an important wreck near Popes Eye, lie near the park.

The southern bay was also an area of concern to the emerging colony as a potential route for invasion by foreign powers expanding their influence in the region in the latter half of the 19th century. Funded largely by gold,  numerous forts were constructed, some of which are still used by the Department of Defence.

Popes Eye was established as the base of a fortress that was never completed. Alongside the artificial island called South Channel Fort, the extensive fortifications at both Point Nepean and Queenscliff, and a fourth fort built on Swan Island, Popes Eye was intended to protect the entrance to the bay, although by the time the other forts were completed, it was made obsolete by the range of guns from the other locations.