The present study aimed to investigate the mineralogical and morphological properties of two South African clays, namely bentonite and kaolin. These clays are mined in specific regions of the country but have not been fully characterized in terms of their properties for potential application in a number of industries. Bentonite was found to have a larger specific surface area, pore size, and more interchangeable cations than kaolin. The bentonite was also identified as Na-bentonite due to the huge Na content present in the clay. The powder X-ray diffraction (PXRD) patterns revealed that both clays are crystalline, together with the Fourier-transform infrared (FTIR) spectrophotometer results; presumably, some impurities of quartz could be present in the clay materials. The most prevalent functional groups present include Al-OH, Si-O-Mg, Si-O, and Si-O-Al groups. The surface charge of bentonite was consistently negative across all pH values, indicating its potential for adsorption applications. On the other hand, kaolin exhibited a negative charge at pH values greater than 2.4. The scanning electron microscopy (SEM) images provided visual evidence of the presence of pores in the clay structures, which supported the Brunauer–Emmett–Teller (BET) results classifying both bentonite and kaolin as mesoporous and macroporous materials. The particle size analysis revealed a broad distribution for bentonite and a bimodal distribution for kaolin. Overall, the clays revealed interesting features that can be useful for application in several industries, for example, in the treatment of wastewater. Further research and development can explore their potential to address environmental challenges, particularly the application of bentonite and kaolin in water treatment processes to remove toxic metal ions.