Methyl tert-butyl ether (MTBE) is a contaminant of concern to groundwater resources due to its persistence in subsurface environments. MTBE appears to be degraded readily in the presence of oxygen but is recalcitrant under the anaerobic conditions prevalent in the subsurface, and can be converted into the more toxic compound tert-butanol (TBA). As ethanol is being promoted as a renewable fuel and a replacement for MTBE in gasoline formulations, its potential impact on the biodegradation of preexisting contaminants and on other components of petroleum must be examined. The purpose of this study is to investigate the effect of ethanol release on existing MTBE plumes and the fate of TBA under sulfate-reducing conditions. Our results suggest that TBA, MTBE and ethanol-induced methane concentrations are strong determinants of the composition of the indigenous microbial community that develops during MTBE transformation. Some of the changes in microbial communities induced by ethanol may be long lasting, thus potentially altering the natural attenuation capacity of the impacted aquifer.