Thanks to the vast range of habitats in the Jervis Bay Territory over 460 native plants have been recorded. A number of plant species in the park have significant conservation status and warrant special protection because of their rarity. These species are protected under various inventories and schedules.
Forest communities in the park are dominated by blackbutt Eucalyptus pilularis and southern mahogany E. botryoides, with a wide variety of native shrubs, ferns and grasses. Relic rainforest communities, which are generally found in wet gullies within forest communities, are dominated by hard corkwood Endiandra sieberi and lilly pilly Acmena smithii. Native poplar Omolanthus populifolius, blueberry ash Elaeocarpus reticulatus, bastard rosewood Synoum glandulosum and cabbage tree palm Livistona australis also occur. Ferns and creepers are common ground cover species in the rainforest gullies.
Woodland communities in the park are dominated by silvertop ash E. sieberi and bloodwood E. gummifera. Woodland understories are composed mainly of heath banksia Banksia ericifolia and old man banksia B. serrata and the grass tree Xanthorrhea australis also occurs.
Common heath species occurring in the park include B. ericifolia, dagger hakea Hakea teritifolia, Manuka Leptospermum scoparium, Xanthorrhea resinosa and Allocasuarina distyla. Coastal scrub communities are dominated by coastal tea tree L. laevigatum. Sporobolus virginicus, Stipa sp. and Zoysia macrantha dominate grassland communities on Bowen Island.
The region has approximately thirty saltmarsh species. There are two species of mangrove in the park: grey mangrove Avicennia marina and river mangrove Aegiceras corniculatum. Subtidal and intertidal platforms support a diversity of rocky reef algae with Hormosira, Ecklonia, Sargassum, Phyllospora and Cystophora being the dominant genera.