Lapalala is mostly underlain by acid, ancient sandstones of the Kransberg Subgroup of the Waterberg Group. More recent intrusions of basic norite/epidiorite are found in the central part.

Generally, soils resulting from the sandstones are dystrophic, meaning that they are extensively leached and nutrient poor. Soils derived from the basic intrusive substrate are more clayey and nutrient rich.

A total of eight different land types have been identified, which is an indication of the heterogeneity, and thus habitat diversity, of Lapalala.