The geological history of Southern Kakadu is very different from that of northern Kakadu. The overall geological evolution is the same, but the period between the deep weathering of the ancient land surface (the Pine Creek Geosyncline) and the deposition of the Kombolgie Formation sandstone was marked by intense faulting, granite intrusion and volcanic activity.
1860 million years ago a rift valley was formed by faulting along a major fracture in the earth's crust. This valley was about 25 kilometres wide and at least 120 kilometres long and ran parallel to the current South Alligator River valley. The faults allowed lava to reach the surface and erupt as a chain of volcanoes. Rivers running through this newly evolving terrain eroded the volcanic rocks and redeposited them as gravel. They also eroded much older rocks brought to the surface by the faulting, to form unusual conglomerates with a pebbly mixture of many different types of rocks. Eventually the valley filled up with sediments, which were subsequently folded, and the 'softer' rocks eroded into a low but fairly rugged landscape with jagged upturned ridges. Later, the Kombolgie Formation sandstone was deposited over them, forming a huge sedimentary plain
Sediments deposited under the Mesozoic sea, 140 million years ago, are well preserved in the south of the park as densely wooded tablelands. They are easily seen south of the Kakadu Highway near the Mary River ranger station. In some places the eroded cliffs are up to 30 metres high and composed of white or brown sandstone or siltstone. They are strongly weathered and commonly capped with laterite. The rocks contain rare fossils mixed with wood and plant fragments.
50 million years ago, during the Eocene epoch, further movement along the ancient faults in southern Kakadu formed local depressions and shallow freshwater swamps. Rocks developed under these conditions formed outcrops near the headwaters of the South Alligator River. Rocks of this age are uncommon in northern Australia, and this small area is of some scientific interest. Drilling has revealed the siltstone sediments to be about 70 metres deep and to contain fossilised spores from the palm trees that once grew there.