The determination of NPECs and their related compounds were performed by LC/MS. Degradation of NPECs occurred 4–7 days after the start up of tests with producing a concomitant of shorter chain NPECs. The long-chain NPECs mixture demonstrated a higher degradation rate than that of shorter ones. In comparison with the fresh secondary effluent system, the NPEOs enriched one showed a much slower NPECs degradation. No nonylphenol or NPEOs was detected during our survey. The results in this study could provide some useful information for the comprehensive understanding of the environmental fate of NPEOs.