From the lancewood forests which clad the tops of sandstone hills to the tall gallery forests flanking the Wilton River, Wongalara features a wide range of ecosystems that are poorly protected elsewhere . Ancient sandstones and shales have been sculpted by centuries of summer rains into a highly dissected landscape with variation evident at every scale. Scarp edges, protected gullies, jagged boulder slopes, gravel plains, wetlands, braided streams, shallow lakes, river flats and black soil plains all support distinct assemblages of plants and animals.
A broad plateau covered in a variety of open woodland communities, and supporting permanent wetlands dominates the north western part of the property. Mount Throsby (230 metres)dominates the western edge of this plateau where the sandstone breaks away into cliff edges, gullies and ravines cut by tributaries of the Jalboi River.
The northen part of Wongalara is formed by the wide valley floor of the Mainoru River, the waters of which flow from west to east in numerous channels, separating and rejoining in a braided pattern to nourish an extensive system of billabongs and gallery forests. Flanking the Mainoru River valley are wide alluvial flats that support a mosaic of grasslands and open woodland.
In the east, the Mainoru River joins the Wilton river, which has a different character. Flowing through Wongalara from north to south, the Wilton occupies a more deeply incised valley with long still waterholes shaded by stately Melaleucas interspersed with tumbling rocky rapids. During summer floods, water rises out of the valley and spreads in a continuous sheet over kilometres of the flood plain. Here the elevation is only 40 metres above sea level.