The southern hills and ridges cover a large area in the south of the park, including the headwaters of the South Alligator River. Rocks here have been exposed from beneath the retreating Arnhem escarpment; they are of volcanic origin and are extremely old (2500 million years). These landforms create a diversity of habitats and the presence of plants and animals that do not occur anywhere else.
This landform is characterised by rugged strike ridges separated by alluvial flats. Its features can be easily observed from the top of Gunlom Falls and on the Yurmikmik walking tracks.
In the South Alligator valley there is a juncture of two biogeographical systems: that associated with the Arnhem Land plateau and that associated with the Marrawal plateau (which extends towards Katherine Gorge). The result of this is a large variety of habitats, great species diversity and large numbers of uncommon or endemic species.
Among the animals that are difficult to see are the brightly coloured hooded parrot, the endangered Gouldian finch, the vulnerable red goshawk, and nocturnal animals such as Calaby's mouse and the Kakadu dunnart. Among the animals that are more commonly seen are the black-breasted buzzard (a kite that is easily identified because of the white 'bulls-eyes' in its wings) and the antilopine wallaby (often confused with the red kangaroo).
The habitats of the southern hills and basins support several endemic plants-plants not found anywhere else in the world. One example is the untidy Eucalyptus koolpinensis, known from only two populations near Jarrangbarnmi (Koolpin Gorge).
Perhaps the most noticeable plant in the woodlands of the south of the park is the salmon gum (Eucalyptus tintinnans). When this tree sheds its old white bark it exposes a beautiful salmon-coloured bark, which gradually fades to white and is shed the following year.
- Freshwater mangrove Abrringtonia actuangula An-galnggi
A small, spreading tree that grows on the banks of freshwater creeks, rivers and swamps. It develops hanging, bright-red flowers between September and December. It is also known as the 'itchy tree': small caterpillars feed on the leaves during the wet season and cause localised skin irritation if touched.
- Silver-leafed paperbark Melaleuca argentea Gun-god
A large, spreading tree commonly seen along the waterways. Its pale-yellow flower spikes appear mainly between June and October and produce a sickly sweet fragrance that attracts many animals.
- Water pandanus Pandanus aquaticus An-djimjim
Commonly grows along the banks of permanent freshwater streams. Its fruit is inedible.
- Yellow bladderwort Utricularia vulva
A small orchid-like plant that grows along sandy creek banks.