The recycling process is applied in many water treatment plants (WTPs), although this process can lead to adverse effects. The effect of the recycling process on the characteristics of dissolved organic matter was evaluated based on a fluorescence excitation-emission matrix using the peak-picking technique and self-organizing map (SOM). In this study, an evaluation of two WTPs, one with and one without a recycling system, was carried out. Both WTPs show moderate efficiency during the coagulation–flocculation process in removing DOC, fulvic acid-like, humic acid-like, and tryptophan-like substances. The recycling process causes increased values of fulvic acid-like, humic acid-like, and tryptophan-like substances and specific ultraviolet absorbance (SUVA) after the filtration process of about 31.0%, 35.7%, 22.2%, and 6%, respectively. Meanwhile, the WTP without recycling showed a reduction in the level of fulvic acid-like, humic acid-like, and tryptophan-like substances and SUVA by 23.3%, 52.9%, 27.8%, and 21.1%, respectively. Moreover, SOM analysis based on the peak-picking technique can determine differences in sample clusters due to the recycling process.