Humpback whales (Megaptera novaeangliae) can be found in Port Phillip Bay. They are known for their acrobatic breaching behavior and can be seen migrating past Victoria each year.  Humpback whales migrate from Antarctica to warmer waters near the equator to breed in winter. They can be seen in large numbers passing Wilsons Promontory Marine National Park. Their migration paths are some of the longest of any mammal.

Common dolphins
The Port Phillip Common Dolphin Project tracks the number of common dolphins in the bay. In 2020, 2021, and 2022, the average number of dolphins in the bay was 58. In 2023, at least six third-generation calves were born. Common dolphins have moved from near Mornington to the Bass Strait waters near Wonthaggi.

Burrunan dolphins
Burrunan dolphins are a unique species of dolphin that are endemic to the southeastern coast of Australia. The Burrunan name comes from an Aboriginal word meaning "large sea fish of the porpoise kind". In 2011, Burrunan dolphins were classified as a separate species from the Common Bottlenose Dolphin. Port Phillip Bay has a resident population of about 120 Burrunan dolphins. 

The "sea dragon" found in Port Phillip Bay is the Weedy Seadragon (Phyllopteryx taeniolatus), a fish closely related to the seahorse, which is considered the official marine emblem of Victoria, Australia; it's known for its unique seaweed-like appendages that help it camouflage in the kelp forests and seagrass beds where it lives, and can often be spotted around piers and jetties in the bay, particularly near Portsea Pier.  

Port Phillip Bay is home to several seal species, with the Australian fur seal being the most prominent. These seals are known for their distinctive appearance, with males having a dark grey-brown fur coat and females having a lighter, white-yellow throat. They also exhibit a unique breeding pattern, with females typically giving birth to pups in the summer months (October-December).