Water supplied to customers must be safe and fit for purpose. It is thus important that the water from water treatment plants (WTPs) meets World Health Organization standards or local standards such as the South African National Standard, before distribution. This study focuses on the treatment of natural organic matter (NOM) in South African WTPs. The problems associated with NOM include: (1) it affects the organoleptic properties of water; (2) increases coagulant demand; (3) reacts with chlorine to form disinfection by-products and (4) causes membrane fouling. The aim of the study was to characterise the NOM composition of various water sources. Specifically, the objectives were: (1) to assess the character of NOM in selected regions of South Africa; and (2) to evaluate the NOM removal efficiencies of the selected WTPs. To achieve these, various characterisation techniques were used to determine parameters such as dissolved organic carbon, ultraviolet absorbance, specific ultraviolet absorbance, and dissolved organic matter, using fluorescence excitation-emission matrix spectroscopy. The character of NOM evolved throughout the treatment process as a result of coagulation, sedimentation and filtration processes. As indicated by SUVA, a decrease in the hydrophobic fraction of NOM from raw to final water was observed, except for plant C2 in Region C where a drastic increase in SUVA from 1.26–31.95 L/mg.m was observed, indicating an increase in the hydrophobic compounds in water. All WTPs were shown to have different removal efficiencies because of the character of NOM in the raw water and the coagulation conditions used.