The fuel oxygenate methyl tert-butyl ether (MTBE) was first introduced in the 1970’s to improve gasoline combustion efficiency and reduce emission of harmful gases. However, it has caused groundwater contamination in Denmark and in many locations worldwide through accidental releases from leaking underground gasoline storage tanks and pipelines. Both laboratory experiments and mathematical computer models were used to acquire knowledge on the scientific and engineering aspects related to the use of bioreactors for removal of MTBE from contaminated groundwater. Results from kinetic parameter estimations showed that the MTBE degraders have very long doubling times which are in the region of 5 – 10 days at 18 °C. This means they are some of the slowest growing microorganisms. The low growth rate was shown to result in out-competition of MTBE degraders by other faster growing species such as ammonium or benzene, toluene, ethyl benzene and xylene (BTEX) oxidizers, which can be present together in a single system. The competition resulted in reduced and/or delayed degradation of MTBE when there were limitations of oxygen or space in the reactor. The fraction of biologically active (BA) MTBE degraders is a reactor is an important quantity for monitoring and optimizing bioreactor performance. A kinetic method was developed to determine the fraction of BA MTBE degraders in bioreactors. Application of the procedure to the PBR used in this study showed that fraction of BA MTBE degraders was only about 10% of total volatile solids in the system. Anaerobic degradation of MTBE was also investigated; it was shown that this is not a feasible engineering option to be applied for MTBE removal from groundwater. It was shown that toxicity of MTBE was not the reason for recalcitrance observed under anaerobic conditions. Overall, the studies showed that despite the effects of competition, fixed film bioreactors can be successfully applied to remove MTBE from ground water to meet the current Danish drinking water regulatory requirement of 5 ppb or even lower.