The park encompasses approximately 840 ha of Jervis Bay waters, and area which comprises approximately seven per cent of Jervis Bay and 13 per cent of the total area of the park. The marine environment of Booderee is excellent representation of largely pristine marine environments of the southeastern temperate region of southeast Australia and is characterised by a wide range of tidal and subtidal habitats. These include shallow rock reefs and sand zones, seagrass meadows, deeper silty sand flats and deep water rocky reefs, cliffs, platforms, blocks, boulders and caves.
The high water clarity of the bay is due to the following factors:
- no major rivers flow into the Bay so very little sediment or other river-borne material is deposited;
- the entrance is flanked by rocky coast with no beaches of any size and the cliffs plunge straight into deep water for most of their length;
- no heavy industry is present in the Bay; and
- a moderate degree of urban development means there is limited sewerage discharge.
The intertidal rock platforms of Bowen Island are particularly significant as they harbour a great variety of intertidal organisms including large numbers and varieties of sea urchins, crabs, abalone, oysters and other organisms depleted elsewhere by human collection and foraging. There are few if any other areas where such a diversity of marine habitats and biota occur in such a small and easily accessible area, situated close to major population areas. Many species present in the marine environment are at the northern and southern limits of their ranges.
Bowen Island also supports a substantial colony of the little penguin Eudyptula minor, and breeding colonies of three species of shearwater - making it of high conservation significance.
The clear waters of the Bay enable the growth of extensive seagrass beds and support a rich diversity of marine life. The seagrass beds contain three genera: Posidonia, Zostera and Halophila. The seagrass areas are of special interest as they rank fifth of the 133 estuaries in terms of total seagrass species found in NSW. Due to the clarity of the Bays waters and deeper penetration of light some plant species (such as seagrass Posidonia sp.) are located at greater depths than expected. These areas provide habitat for a diversity and abundance of fish and macro invertebrates. Subtidal and intertidal platforms support a diversity of rocky reef algae with Hormosira, Ecklonia, Sargassum, Phyllospora and Cystophora being the dominant genera.
The littoral communities of the park are of both local and statewide significance. They include mangrove communities along Sussex Inlet and south of Whiting Beach; saltmarsh communities at Flat Rock Creek and on the southern section of Bowen Island; and intertidal rocky platforms.
The mangrove communities provide habitat for a number of intertidal estuarine organisms, fish and terrestrial species. They also aid in sediment stability and enhance productivity in estuarine ecosystems. Saltmarsh communities are of high conservation value as bird feeding areas.
The rock platforms contain pools, which are regularly exposed at low tide. The intertidal rock platforms of Bowen Island harbour large numbers of sea urchins, crabs and other organisms depleted elsewhere by human collection and foraging.