Water samples from Waiora Drinking Water Treatment Plant in New Zealand were analyzed using excitation‐emission matrix fluorescence spectroscopy (EEMS) and parallel factor (PARAFAC) analysis to evaluate organic matter removal across the plant. The assessment also included the individual granular activated carbon (GAC) filters since the filters had varying media ages due to partial media replacement over a 10‐month period, presenting a unique assessment opportunity. PARAFAC analysis identified humic‐like, tyrosine‐protein‐like, and tryptophan‐protein‐like components representing fluorescent dissolved organic matter groups. The humic‐like component strongly correlated with total organic carbon (TOC) concentration and removal was significantly influenced by filter media age. However, protein‐like components had minimal TOC correlation and were not effectively removed by the overall plant treatment irrespective of filter media age. These findings have implications for disinfection, taste and odor, and bacterial regrowth and require an improved media replacement strategy. Further study of the protein‐like components is required.