Measuring the surrogate parameters total organic carbon and dissolved organic carbon (TOC/DOC) is not adequate, alone, to reveal nuances in organic character for optimizing treatment in potable water reuse. Alternatively, analyzing each organic compound contributing to the surrogate measurement is not possible. As an additional analytical tool applied between these extremes, the use of excitation-emission matrix fluorescence spectroscopy with PARAllel FACtor (EEM-PARAFAC) analysis was investigated in this research to track categories (components) or families of organic compounds during treatment in recycled water schemes. Although not all organic molecules fluoresce, many do, and fluorescence helps track their fate through water treatment processes. The sites investigated in this research were Lake Lanier, in Gwinnett County, Georgia, USA; the F. Wayne Hill Water Resources Center (FWH WRC) advanced wastewater treatment facility; and two pilot facilities operated in parallel representing the current indirect potable reuse (IPR) scheme as well as a pilot that evaluated direct potable reuse (DPR). A four-component nonnegativity PARAFAC model—elucidating protein-like (including tyrosine- and tryptophan-like fluorescence in a single component), soluble microbial product (SMP)-like, fulvic-like, and humic-like components—was fitted to the data. Each of the four components was spectrally and mathematically separated, implying that the fluorescing SMP-like component was not comprised of protein-, fulvic-, or humic-like components. PARAFAC excitation loadings with dual (double) pairs of fluorescing regions centered at the same emission wavelengths but different excitation wavelengths oriented parallel to the excitation axis and perpendicular to the emission axis were attributed to individual PARAFAC components. Significantly, the observation of PARAFAC emission loadings with multiple peaks—where the protein-like component exhibited fluorescence in both protein and fulvic/humic regions—is proposed to signify an intermolecular energy transfer (< 10 nm). Correct identification of EEM-PARAFAC components is fundamental to understanding water treatment.