A pilot-scale research investigation examining treatment technologies including coagulation, ion-exchange, activated carbon and membrane filtration and their impact on water quality coincided with a period of extensive variability in source water character. Distinct water quality periods as a result of extreme climatic conditions from drought to flood were observed and the natural organic matter (NOM) removal examined using a suite of organic characterisation techniques from simple ultraviolet (UV) absorbance to more advanced spectroscopic and chromatographic methods. The low specific UV absorbance (SUVA) and apparent molecular weight (AMW) distribution of the drought-impacted NOM was recalcitrant to coagulation with significant improvement in NOM removal resulting from the multi-step treatments. Among a number of discernible changes, floodwaters introduced high AMW, UV-absorbing NOM of terrestrial origin, which was shown to be more amenable to coagulation. Nevertheless the application of multi-step treatments resulted in further reduction in both the concentration and diversity of organic components. Filtration through granular activated carbon was observed to be the most variable treatment technology across the investigated period due to diminishing adsorption capacity. Conversely, the dual stage membrane filtration was shown to remove a broad range of organic matter, regardless of source water NOM concentration and character.