The aim of this study was to investigate nitrogen mass balances occurring inside full-scale BNR activated sludge systems, with special attention to colloidal and dissolved organic nitrogen (CON and DON) transformations. For this purpose, laboratory experiments were carried out using process biomass from two large BNR plants in northern Poland. Two parallel batch reactors were operated in a 3-phase (anaerobic/anoxic/aerobic) cycle. In one reactor, the settled wastewater without any pretreatment was used, whereas the settled wastewater after coagulation-flocculation (to remove colloidal and particulate fractions) was added to another reactor. The chemical pretreatment of settled wastewater with ZnSO4 did not adversely affect the observed nitrification rates in the (last) aerobic phase. It caused, however, a reduction of denitrification rates in the anoxic phase. Moreover, the chemical pretreatment did not appear to generally decrease DON but decreased CON. DON was explicitly produced in the aerobic phase and organic nitrogen conversion also occurred at a significant rate in the anoxic phase with biodegradable COD consumption and solids hydrolysis. The inorganic N mass balances revealed N losses up to approximately 10% which could be attributed to a few novel pathways of nitrogen removal, most likely aerobic denitrification or simultaneous nitrification/denitrification.