Some of the protected and threatened species found in the marine park include grey nurse shark, black rockcod, sea turtles, whales and shorebirds.
- The park contains important areas of habitat for the endangered grey nurse shark, with critical habitats at The Pinnacle, Big/Little Seal Rocks and Little Broughton Island.
- The shy black rockcod belongs to the cod and Grouper family. It can be found hiding along rocky reef crevices.
- The park is also home to green, loggerhead and hawksbill turtles, with juvenile green turtles the most abundant within Port Stephens estuary. Occasionally leatherback turtle are spotted offshore.
- The vulnerable Gould's petrel (Australia's rarest endemic seabird) breeds only on Cabbage Tree and Boondelbah Islands off the coast of Port Stephens. The species feeds surface fish, small squid and krill in oceanic waters over a wide area.
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