Natural attenuation of anaerobic aquifers contaminated with tetrachloroethene (PCE) often results in the accumulation of the intermediates cis-dichloroethene and vinyl chloride (VC) which are even more toxic than the parent compound. Reasons for this accumulation were investigated in a PCE-contaminated aquifer in which VC accumulation has previously been shown to occur using stable isotope techniques. Multifactorial analysis of bacterial community structure data and environmental variables showed that in general terminal electron-accepting processes were shaping the bacterial community structures. Both VC and Fe(III) reduction were key but antagonistic terminal electron-accepting processes. The phylogenetic affiliation of terminal restriction fragments (T-RFs), together with correlation analyses, showed that T-RFs having significant correlation with VC reduction were closely affiliated to the genus Dehalococcoides and to uncultured bacteria belonging to the “Lahn Cluster” within the class Dehalococcoidetes. A T-RF that negatively correlated with a “Lahn Cluster” T-RF was affiliated to the genus Rhodoferax that contains members identified as iron-reducing bacteria. The higher affinity of Fe(III)-reducing bacteria for hydrogen compared with VC-reducing bacteria might explain why VC accumulated locally at the studied site. In conclusion, the combination of molecular and numerical ecology approaches was helpful to identify reasons for the accumulation of toxic dechlorination intermediates and could become a useful tool for characterizing contaminated sites in general.