All the rocks at Malolotja are extremely old and rank amongst the oldest on earth. They are part of the "archaean basement" of what has later become the African continent. Entering the park, the high ground adjacent to the Piggs Peak to Motshane road is made up of granite, an igneous rock which has cooled deep in the earth's crust and has for most of its history been covered by later rocks, only recently being stripped of its cover and appearing at the surface. The granite, known geologically as the Lochiel Granite, has a rough, speckled appearance, with obvious white crystals of quartz, orange crystals of feldspar and black crystals of biotite mica. Using the radioactivity trapped in the newly formed rock, the Lochiel Granite can be dated to 3029 million years old, almost three quarters of the way back to the assumed formation of the earth. Long after it had formed a solid mass, it was intruded by wall-like dikes of dolerite, cooled from a liquid magma which forced its way into cracks in the granite.

But the Lochiel Granite is not the oldest rock in the reserve. The remaining three-quarters of Malolotja, including the whole of the Malolotja Valley, Ngwenya, and the high ground to the west, are rocks of the Swaziland Supergroup, amongst the oldest metamorphosed sedimentary rocks in the world. These rocks, which once included sandstones and mudstones as well as surface volcanics were laid down horizontally, layer by layer, in the deep ocean of the primaeval earth about 3500 million years ago. As such, they are thought to contain fossils of the earth's oldest life forms - blue-green algae. These are found in the green cherts exposed in the Nkomati gorges. After they were laid down as a series of horizontal strata, the whole group was drawn into the earth's crust and metamorphosed, cooked by the relatively low heat and pressure of the mantle, where they were metamorphosed into highly resistant quartzites and shales, gneissitic rocks and talc schists. Further, these transformed rocks were folded and cracked, faulted and tilted until now they have reappeared at the surface as a series of almost vertical but dislocated bands.

The Swaziland Supergroup is divided into three subgroups, the oldest of which is the Onverwacht Group. This is found in a broad hemicircle of the upper Malolotja Valley, Forbes Reef and the upper Mbuluzi Valley. The main components of the Group seen locally are talc-chlorite and talc-carbonate schists, which have been weakly metamorphosed from original lavas. The schists are extremely soft and they have a pearly appearance and noticeable "soapy" feel, hence the common name "soapstone". The locally made carvings and heads are made from this soft rock, although the finished carvings are often stained to alter the basic greenish white colour. Another similar kind of rock which is also found in the Onverwacht Group is serpentinite which tends to be more fibrous. The best known example of this is the fibrous chrysotile asbestos mined at Havelock near Piggs Peak since the 1930's, and Msauli Mine in South Africa. Waste from this mine is carried down the Nkomati River into the park and deposited as sands, distinctly green in colour. The Onverwacht rocks also contain minute quantities of gold, which has attracted prospectors to the Malolotja area for the best part of a hundred years. The gold is present in such small amounts that mining operations were never long lived, but long enough in one case to see the development of the village of Forbes Reef at the beginning of this century. Barite also occurs in the Onverwacht Group just to the west of Ngwenya in the Londozi Valley. It was discovered in 1937 and mining continued from 1945 to 1976 from small underground workings and shallow quarries.

The second set of rocks in the Swaziland Supergroup are the Fig Tree Group, a layer cake of metamorphosed rocks which include interbedded shales, quartzites, cherts and ironstones. These occur especially at the southern end of the reserve, south of the summit of Ngwenya and again in the north west of the reserve, either side of the Nkomati River. The quartzites were formed by the metamorphosis of original quartz sandstones which welded the granules together to make a rock which is extremely resistant to weathering or erosion. In the Fig Tree Group, the quartzites are usually a bluish black, grainy rock with a hard, glassy appearance. They alternate every few centimetres or metres with shales and ironstones, giving a hard "liquorice allsort" appearance. The contorted nature of these sedimentary beds has meant that the once horizontal rocks are now standing on end like books on a shelf.

At the southern end of the reserve, the rocks have been doubled over in a vertical cross-fold which has led to an enrichment of the haematite-chert ironstones and produced near the surface a pocket of very rich iron ore which has been mined at Bomvu Ridge, Ngwenya. The ore body is divided into 7 ore reserve blocks, each separated by a dike, a fault or by the major axis of the fold deformation. There are important differences in grade and chemical composition between the blocks as well as in thickness, the thickest being the Lion Block in the north. The origin of the iron deposits is uncertain. Goodwin (1964) infers that while the volcanics below were flat lying, fluids migrated up from these which caused chemical transport to the rocks above and the deposition of the carbonate iron formation. The origin of the fluids is uncertain.

The third and youngest set of rocks, still older than the adjacent granites, in the Swaziland Supergroup are yet more layers of ocean floor sediments, metamorphosed and twisted into an upright position. They form the largest area of the reserve and cover a broad zig-zag south from the Nkomati, west across the lower Malolotja Valley, to the summit of Ngwenya. Being the youngest of all the Supergroup, the Moodies Group was formed from the erosional debris of other rocks which now form a quartzite conglomerate. Now metamorphosed, they are blue-black in colour with a gravelly appearance.