Copper ion (Cu2+), a common corrosion product released from copper pipes, is widely present in water distribution system (WDS). Cu2+ was confirmed to be capable to catalyze the decay of monochloramine (NH2Cl), which is a commonly used disinfectant and need to maintain a minimum concentration in WDS. Cu2+ and NH2Cl form a system in WDS and their interaction with other substances in WDS is unclear. In this study, the performance of Cu2+/NH2Cl system on degradation of trace pollutants, taking carbamazepine (CBZ) as an example, in WDS was investigated, and significant promotion on CBZ degradation was observed. The acceleration was due to the generation of Cl, OH and other oxidants, which were identified by scavenge experiments. CBZ degradation in Cu2+/NH2Cl system was highly pH-dependent, because the catalytic effect of Cu2+ can only work at low pH (Cu2+ precipitating at pH > 6.0). The removal of CBZ increased with the concentration of Cu2+ increasing. Water matrix (NOM, HCO3− and Br−) can inhibit the removal of CBZ in Cu2+/NH2Cl system. Further, five disinfection byproducts (DBPs), namely, trichloromethane (TCM), dichloroacetonitrile (DCAN), dichloroacetone (DCP), trichloronitromethane (TCNM) and trichloroacetone (TCP), were detected in chloramination in the presence/absence of Cu2+. Compared with chloramination without Cu2+, the cytotoxicity and genotoxicity of formed DBPs increased significantly in the presence of Cu2+, indicating that the chemical safety in WDS deserves more attention.