Booderee covers approximately 85 per cent of the Bherwerre Peninsula, which is underlain with Permian sandstones, siltstone and conglomerates of marine origin. They are part of the southernmost extent of the Sydney basin sedimentary rocks. Dunes and sandy soils overcap the Peninsula. Bedrock is exposed in cliffs, marine platforms and minor exposures in creeks and dune areas. Lake Windemere and Lake McKenzie evolved when streams were blocked by sand. Bowen Island is composed of the same sandstone type as the Peninsula and slopes sharply from cliffs on the eastern oceanic side down to sea level rock platforms on the western, Jervis Bay side. The sandstone on the Island is covered by windblown sand, which supports a range of vegetation communities.

Other features of geological interest in the park include fossil sites and exposed stone walls of a substantial quarry used to supply stone for the construction of the HMAS Creswell breakwall in 1915.

The sandy soils of Bherwerre Peninsula and Bowen Island are unconsolidated and depend upon the presence of vegetation cover for stability. When vegetation is removed, the soils and sand dunes are readily eroded by wind, water and physical disturbance.

The shallower sand covered sections of Jervis Bay are covered by seagrass meadows.