Booderee National Park is both nationally and regional significant for its natural and cultural values.
The area of Jervis Bay was entered on the Register of the National Estate in 1993 in recognition of its outstanding landscape features, its diversity of flora, fauna and archaeological sites and its value to past and present communities for recreational activities.
The park contains many species that are at the limits of their bio-geographical range. The habitats protect a high concentration of rare and threatened plants and animal species. The park supports a population of endangered Bristle Birds and also the threatened green and golden bell frog. The park protects a significantly large area of species rich heath, a diversity of wetlands and extensive saltmarshes. the park also protects the largest Posidonia seagrass meadows in New South Wales. The area is also one of the State's outstanding scenic locations.
The Botanic Gardens, a former annex of the Australian National Botanic Gardens, contains a significant collection of plants collected over the last fifty years, and is unique in its presentation of regional Koori plant utilisation.
The area supports a population of bottlenose dolphins and the bay is registered as a type locality for many marine invertebrates and algal habitats. The park protects coastal dune systems and their associated habitats which are otherwise disturbed or potentially threatened in the region. The area is scientifically valuable as it has not undergone degradation like the Sydney area. The preservation as a southern representative of the sandstone ecosystems is highly important.
In recognition of the bay's outstanding natural and recreational values, the New South Wales Government declared the state waters of Jervis Bay as a Marine Park jointly managed by New South Wales National Parks and Wildlife Service and New South Wales Fisheries.