BACKGROUND: An aerobic upflow fixed bed reactor (UFBR) was densely colonized by a bacterial consortium, obtained from gasoline polluted waters, able to mineralize MtBE and BTEX. The system was studied in order to determine its capability to degrade the MtBE present in prepared solutions and in real contaminated aquifers and was operating for more than a year. RESULTS: Efficient colonization of the reactor took about 50 days, utilizing bacteria grown in continuous culture in a fermenter connected to the UFBR. During the study the influence of feed concentration of MtBE, temperature and hydraulic retention time (HRT) was analyzed. The system, running at 18 degrees C on synthetic medium, was fed at an influent MtBE concentration of 27.8 mg L-1 with HRT of 5 h showing 99.98% of MtBE degradation. When working with polluted groundwater, the system achieved 100% BTEX degradation and 99.34% MtBE degradation. CONCLUSION: The UFBR was tested on synthetic medium spiked with MtBE and on groundwater contaminated with MtBE and BTEX at concentrations of 50-60 ppm and a few ppm, respectively. The reactor responded efficiently showing great flexibility and capability of adjustment to different operating conditions with MtBE degradation of nearly 100%. (C) 2009 Society of Chemical Industry