Natural organic matter (NOM) is a complex heterogeneous mixture of humic (HS) and non-humic substances which are widespread in the aquatic environment. Other constituents are amino acids, aliphatic and aromatic hydrocarbons containing oxygen, nitrogen and hydroxyl groups. It is the combination and proportions of these motifs which give NOM its overall polarity and reactivity. Its main origins include soils, residues of fauna and flora, microbial excrements and anthropogenic faecal loads, agriculture activities and urban landscapes. Due to the different origins of the precursor material and the extent of transformation it undergoes, the composition of NOM in different water bodies varies. Characterization methods for NOM can be divided into three broad categories namely: (i) direct measuring methods, which measure the amount of organic matter in the sample; (ii) spectrometric methods, which measure the amount of radiation absorbed and or released by chromophores; and (iii) fractionation methods, which separate NOM according to size and polarity. South Africa has 6 distinct water quality regions, and each region has a unique NOM character and quantity. Existing water treatment plants do not remove NOM to levels low enough to inhibit the formation of disinfection by-products (DBPs). Currently, research is focusing more on the use of alternative techniques for NOM removal; these include advanced oxidation processes (AOPs), nanomaterials, and ceramic membranes. While NOM is well studied in other parts of the world, to the best of our knowledge, there is no state-of-the-art investigation of the occurrence and removal of NOM in South African source waters. This review aims at (i) synthesizing literature on the nature, occurrence and ecological impact of NOM, (ii) evaluating the removal of NOM in the six different water quality regions of South Africa, and (iii) suggesting novel approaches that can be used to remove NOM in South Africa.