Only a relatively recent addition to the national parks registry, Bungonia was originally protected as a water reserve to prevent contamination of the Shoalhaven River in the mid-late 19th century.

Archaeological evidence of campsites has been found on the main plateau, along with limestone dolines that contain the remnants of edible plants consumed by Aboriginal peoples.

The formations in Bungonia are part of the Lachlan Fold Belt which is made up of metamorphosed ordovician and devonian sandstones, shales and volcanic rocks.

[6] The rock sequence in Bungonia is highly mineralised and part of a larger series of formations which contain gold deposits of economic importance to the region.

[6] A wide dry plateau makes up a great deal of the land area in the park with many cliffs and gorges occurring near prominent water-ways such as the Shoalhaven River and Bungonia Creek.

Soil in Bungonia is mostly shallow structured organic loams which lie atop of the limestone and basalt plates which form the main plateau.

[6] Like much of the southern portion of the Great Dividing Range, black she-oak (allocasuarina littoralis) is common to lower canopy and regeneration areas.

Other fauna in the park include the vulnerable large bent-wing bat which breeds in many of the caves in the cooler parts of the year.

Monitor lizards, echidnas, wombats, wallabies, and small populations of koalas and spotted-tail quolls also inhabit the park.

[7] Environmental issues in the park are most prominent in the koala and spotted-tail quoll population, both of which are endangered by habitat destruction and feral animals.

[8] Small woodland bird species such as the hooded robin and varied sittella have also come under threat due to habitat destruction caused by mining projects in the region.

This has led to NPWS regularly closing off the Drum and Grill caves in order to protect the population during their vulnerable breeding season.

[9] A large limestone quarry operated by Boral Limited immediately to the north of the Bungonia Gorge has also raised concerns regarding the preservation of significant geology in the area.

The quarrying run-off poses a risk to water sources in the area whilst land clearing and subsequent erosion has threatened certain parts of the gorge structure and the eucalypt forest which covers the hills surrounding the valley.

Their current activities involve filling in the southern end of the pit and re-vegetating their emplacements with native species whilst they continue to quarry the northern section.

Numerous accidents have occurred in Bungonia National Park, partly due to its popularity with cavers and climbers, as well as its lack of marked tracks and dense bushland.