Industrial wastewater containing heavy metals that enters waste water treatment plants inescapably has a toxic impact on biological phosphorus removal process. The long-term effect of Cu (II) on the performance of the enhanced biological phosphorus removal system was investigated for about 100 days. 0.5 and 2.5 mg/L Cu (II) were dosed into two parallel SBR reactors (R1 and R2), respectively. The results showed that 0.5 mg/L Cu (II) did not impact the performance, while 2.5 mg/L Cu (II) significantly influenced its performance, which experienced an acute deterioration stage in the initial couple of days, followed by an unstable period, then a steady-state period. In the steady-state period, the conditions in R2 were more suitable to polyphosphate accumulating organisms than glycogen accumulating organisms. The phosphorus was removed through the transformation of free phosphorus to acid soluble phosphorus, and in R2, its efficiency reached 96.1%, 11.7% higher than that in R1. In cycle study, higher concentration of poly-phosphate, less concentration of glycogen, higher activities of exopolyphosphatase and polyphosphate ldnase were also observed in R2 than that in R1. Crown Copyright (C) 2015 Published by Elsevier B.V. All rights reserved.