ABSTRACT Following drought and successive extreme rain events, there was a significant change in the source raw water quality from Lake Nepean, New South Wales, Australia. This resulted in spikes of up to 400% in true colour, 150% in dissolved organic carbon (DOC), and 200% in total organic carbon (TOC) in Lake Nepean, representing a substantial increase of natural organic matter (NOM). This research identified that the predominant organic fraction of the NOM is humic acids, which comprises 71–73% of the DOC in the raw water, despite organic matter variability by rainfall in the catchment. The composition of NOM does not largely change; however, the concentration of the humic acid fraction of the NOM in the raw water in a water dam substantially increases during and after a rainfall event in the catchment. The study developed linear relationship models to estimate the changes of humic acids from regular water quality parameters (e.g., true colour, DOC, UV254). This is a novel approach where long-term variability of organic fractions, impacted by forecasted intense and frequent rain events in a water catchment, can be reliably estimated using a statistical model based on historical water quality parameters.