An immobilized microbial process containing anaerobic filters and biological aerated filters (I-AF-BAF) system was used to treat 2,4,6-trinitrotoluene (TNT) red water. The results showed that the system could effectively degrade the organic pollutants in TNT red water, especially 2,4-dinitrotoluene-5-sulfonate (2,4-DNT-5-SO3-), most of which was degraded by the microorganisms in the system. The results of high performance liquid chromatographic (HPLC) and liquid chromatography-mass spectrum (LC-MS) indicated that 2-amino-4-mononitrotoluene(MNT)-5-SO3- and 3-amino-2-MNT-5-SO3- might be the main anaerobic degradation metabolites. As the extra carbon source and electron donor, ethanol played a major role in the biodegradation of TNT red water. In addition, environment scanning electron microscope (ESEM) analysis revealed that many globular microorganisms were successfully immobilized on the surface of the carriers. Further analysis by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) demonstrated that some special bacteria for the degradation of the pollutants in TNT red water might be generated during the acclimatization with TNT red water for 110 days, and they were identified as Hydrogenophaga sp., Exiguobacterium sp., Azospirillum zeae, Rhizobium sp., and iron-reducing bacterium by comparing the gene sequences from Genbank. This study may be useful for the treatment of actual TNT red water loaded with high concentrations of salinity and toxic organic components. (C) 2014 Elsevier B.V. All rights reserved.