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In this study, samples from the Yangtze River, Han River, and Liangzi Lake in Wuhan City were utilized to characterize the formation of disinfection by-products (DBPs) from chlorine-based disinfection residues in drinking water sources. The results indicated that the main DBPs in drinking water sources were trichloromethane (TCM) and trichloroacetic acid (TCAA). The generation of DBPs was significantly positively correlated with oxidative substances, aromatic compounds, pH, and ammonia nitrogen (NH3-N) content in the water. The concentration of TCAA increased from 0 to 2.45 ± 0.31 mg/L when the reaction time increased to 72 h. As the NaClO concentration increased from 5 mg/L to 15 mg/L, the concentrations of TCAA, TBM, and DCAN increased from 2.03 ± 0.04 mg/L, 0 mg/L, and 0 mg/L to 2.49 ± 0.34 mg/L, 0.21 ± 0.07 mg/L, and 0.10 ± 0.04 mg/L before decreasing to 1.75 ± 0.19 mg/L, 0.17 ± 0.07 mg/L, and 0.04 ± 0.05 mg/L, respectively. The orthogonal experimental results showed that Br−, NH3-N, and pH all had significant influences on the TCM generation, whereas temperature affected the formation of TCAA in the Han River. This work reveals the factors influencing the generation of DBPs from chlorine-based disinfection residues, offering a prevention and control method for DBPs in drinking water sources from a theoretical perspective.