To alleviate the eutrophication caused by excessive loading of nutrients, the upgrading of conventional activated sludge (CAS) process to biological nutrients removal (BNR) process has been widely applied in USA. In this study, we found that the dissolved inorganic nitrogen (DIN) release can be effectively controlled by this upgrading, but dissolved organic nitrogen (DON) especially LMW-DON, which now is regarded as another important N source for supporting growth of phytoplankton in coastal water, cannot be removed effectively by BNR systems, especially by four-stage BNR systems. Different pre-denitrification BNR processes have different LMW-DON production rates. A four-stage pre-denitrification BNR releases more LMW-DON in effluent than two-stage pre-denitrification BNR. The higher DON production may be caused by longer anaerobic time. Also, the characteristics of influent influence the formation of LMW-DON in BNR system. Influent with acetate and higher COD concentration can stimulate more DON and LMW-DON release in a BNR process. This suggests that relative regulation should be established to prevent the release of DON. A post-treatment method should be added to remove DON produced by the BNR process.