The increase of fluorescent natural organic matter (fNOM) fractions during drinking water treatment might lead to an increased coagulant dose and filter clogging, and can be a precursor for disinfection by-products. Consequently, efficient fNOM removal is essential, for which characterisation of fNOM fractions is crucial. This study aims to develop a robust monitoring tool for assessing fNOM fractions across water treatment processes. To achieve this, water samples were collected from six South African water treatment plants (WTPs) during winter and summer, and two plants in Belgium during spring. The removal of fNOM was monitored by assessing fluorescence excitation–emission matrices datasets using parallel factor analysis. The removal of fNOM during summer for South African WTPs was in the range 69–85%, and decreased to 42–64% in winter. In Belgian WTPs, fNOM removal was in the range 74–78%. Principal component analysis revealed a positive correlation between total fluorescence and total organic carbon (TOC). However, TOC had an insignificant contribution to the factors affecting fNOM removal. Overall, the study demonstrated the appearance of fNOM in the final chlorinated water, indicating that fNOM requires a customised monitoring technique.