Numerous industries and facilities have been using chlorinated ethenes (CEs) as non-flammable solvents during manufacturing. Massive usage, careless handling and storage, spills and leakages made them one of the most frequent aquifer contaminants. CEs are reductively dechlorinated under anaerobic conditions by dehalorespiring bacteria leading to the formation of harmless ethene as end product. The geographical pattern and the main ecological drivers of the microbial communities involved in these dehalorespiration activities have rarely been investigated yet. In the present study, we made the hypothesis that the chemical contaminants are inducing an important selection pressure on the bacterial taxa resulting in a convergence of the communities present in geographically distant aquifers. Bacterial communities present in five CE-contaminated Quaternary European aquifers (88 samples) were analyzed using a standardized T-RFLP analysis as a meta-analysis. Numerical ecology tools were used for statistical analysis to measure the relations between the bacterial communities and their geographical positions, the local chemical and physical conditions and the contaminant concentrations. The analysis included among others functional principal component analysis (fPCA), Mantel and Tuckey’s HSD tests. Contrarily to our expectations, both latitude and longitude coordinates were significantly correlated with the observed bacterial communities. A significant positive correlation was equally found between bacterial communities and the geographical distances between the aquifers. Moreover, the analysis demonstrated that the observed bacterial communities were structured with an almost identical contribution by both the localization of the aquifer and the local chemical and physical conditions. The chlorinated contaminant concentrations contributed to a much lesser extent to the variability between bacterial communities. Our data suggested the presence of a marked biogeographical pattern and that beneath traditional soil environments aquifers are isolated spatially and inhabited by bacterial communities whose structures are remarkably correlated with their respective habitat. From an ecological point of view, aquifers can be considered as a heterogeneous assemblage of discrete macro- and micro-scale habitats, providing a variety of living conditions, which in turn influence the heterogeneous distribution of the microbial communities and their inherent activities. Compartmentalization and biogeographical patterns allow for the development of ecosystem processes in defined sequences and ensures the development of a high diversity, and hence functional redundancy.