A modified DEPHANOX process including two upflow sludge blanket reactors (USB) (anaerobic-upflow sludge blanket -UASB and anoxic-upflow anoxic sludge blanket -UA(N)SB) and one completely stirred tank reactor (CSTR system was simulated in order to detect the simultaneous removal of dinitrotoulene (DNT), trichlorotoluene (TCT), and nutrients. The phosphorus uptake and nitrification was excessively determined in aerobic CSTR reactor. Influent DNT was transformed to toluene, NH4-N and total aromatic amines (TAA) while TCT was transformed to toluene and dichlorotoluene (DCT) under anaerobic and anoxic conditions. Increasing the volumetric loading rate of DNT and TCT from 18 mg/L.day and 0.35 g/L.day to 60 mg/l.day and 1.2 g/L.day, respectively, resulted in higher COD conversion (70-80%) rates and methane productions (250-300 ml/day) in anaerobic reactor. 90% NO3-N and 87% PO4-P were achieved in anoxic and aerobic reactors at DNT and TCT loading rates as high as 40-60 mg/L.day and 0.8-1.2 g/L.day, respectively. The TAA produced under anaerobic and anoxic conditions were ultimately removed under the aerobic stage. The UASB and anoxic UASB reactor effluents were less toxic relative to the influent when analyzed by anaerobic toxicity tests and specific methanogenic activity tests, indicating that such anaerobic/anoxic aerobic sequential treatments could be able to reduce toxic organics together with nutrient removal.