BACKGROUND: A packed bed bioreactor (PBBR) activated with an indigenous nitrifying bacterial consortia was developed and commercialized for rapid establishment of nitrification in brackish water and marine hatchery systems in the tropics. The present study evaluated nitrification in PBBR integrated into a Penaeus monodon recirculating maturation system under different substrate concentrations and flow rates. RESULTS: Instant nitrification was observed after integration of PBBR into the maturation system. TAN and NO(2)-N concentrations were always maintained below 0.5 mg L(-1) during operation. The TAN and NO(2)-N removal was significant (P < 0.001) in all the six reactor compartments of the PBBR having the substrates at initial concentrations of 2, 5 and 10 mg L(-1). The average volumetric TAN removal rates increased with flow rates from 43.51 (250 L h(-1)) to 130.44 (2500 L h(-1)) gTAN m(-3) day(-1) (P < 0.05). FISH analysis of the biofilms after 70 days of operation gave positive results with probes NSO 190 ((beta ammonia oxidizers), NsV 443 (Nitrosospira spp.) NEU (halophilic Nitrosomonas), Ntspa 712 (Phylum Nitrospira) indicating stability of the consortia. CONCLUSION: The PBBR integrated into the P. monodon maturation system exhibited significant nitrification upon operation for 70 days as well as at different substrate concentrations and flow rates. This system can easily be integrated into marine and brackish water aquaculture systems, to establish instantaneous nitrification. (C) 2011 Society of Chemical Industry