A laboratory-scale bioreactor study was conducted to characterize differences in nitrification function in main-stream reactors due to bioaugmentation from side-stream reactors treating reject water. The objective was to evaluate how configuration of a suspended growth side-stream bioreactor impacts nitrification function in the main-stream bioreactor. A bioaugmentation effect was not observed in main-stream reactors operated at warm temperatures. Complete oxidation of ammonia to nitrate was observed in the bioaugmented and control main-stream reactors although nitrite accumulation was observed in each case. Furthermore, respirometry did not reveal superior kinetics in bioaugmented reactors operated at warm temperatures. At cold temperatures bioaugmentation may have stabilized ammonia oxidation in main-stream reactor B2 bioaugmented from a PFR side-stream. Complete ammonia oxidation was observed for most of cold period of operation in the main-stream bioreactor B2. Furthermore, respirometry revealed a higher rate of ammonia oxidation and more stable nitrite oxidation compared with the control bioreactor.