A parallel factor (PARAFAC) analysis approach was used to study the character and composition of dissolved organic matter (DOM) in a multicoagulant (two aluminum-based coagulants) full scale drinking water treatment plant. A three year, long-term assessment was conducted based on deconstruction of the excitation-emission matrices (EEM) of over 1000 water samples collected before and after parallel coagulation treatment basins. Two humic moieties and a protein-like group were identified in the raw and treated waters. Apportionment of fluorophores was established using a novel approach based on the overall fluorescence intensity (OFI) of PARAFAC components. Uncorrected matrix correlation (UMC) revealed minimal changes of the fluorescence moieties after treatment (UMC > 0.98), and a comparable effect of both coagulants on the structure (UMC > 0.99) and distribution of these groups. Coagulation increased the proportion of the protein-like fluorophore and preferentially removed a humic-like group irrespective of the coagulant. Preference for this moiety was supported by a coagulant-affinity factor derived from the association between PARAFAC components after treatment. The suitability of a PARAFAC-based approach for coagulant evaluation/selection was demonstrated when compared to a dissolved organic carbon (DOC)-based criterion. This paper contributes to the understanding of the behavior of PARAFAC components in water treatment processes and presents several approaches for the future monitoring and control of coagulation at full scale treatment facilities.