This study presents an investigation on the fate of natural organic matter (NOM) and its dynamics throughout the treatment train at various drinking water treatment plants (WTP) in South Africa. The characteristics, concentration and removal efficiencies of NOM at various treatment stages on the basis of dissolved organic carbon, UV absorbance, specific ultra-violet absorbance, spectroscopic indices, maximum fluorescence intensity (Fmax), and polysaccharides removal, were studied. The highest polysaccharide concentration was in coastal plants compared to inland plants for the raw water samples. A Parafac model fitting four components was established for the raw waters, and validated based on the split half criteria. The Fmax values of the components was higher for terrestrial humic-like component (C1) and fulvic-like component (C2) than for humic-like components (C3), and for protein-like component (C4). Strikingly, the mean Fmax values for C2 and C3 were higher for plants located on the south west coast of South Africa than the plants located inland. While the humification index and UV254 removal correlated (R2 = 0.797), the correlation between the freshness index (β:α) and UV254 removal was also mild (R2 = 0.787). The removal efficiencies of bulk NOM were higher than for FNOM in the rapid sand filtration (RSF) stage, regardless of the location of the plants, suggesting that the RSF process is more efficient in removing non-fluorescent NOM than FNOM fractions. This study demonstrated the capability of optical methods in characterizing the fate, occurrence and removal of NOM in surface waters.