Chlorinated ethenes (CEs), such as perchloroethene (PCE) and trichloroethene (TCE), are one of the most common class of groundwater contaminants. Aquifers are considered nowadays as dynamic ecosystems, showing multiple interactions between the physical, chemical and biotic components. The assessment of the intrinsic contaminant biodegradation capacities of these complex ecosystems was carried out using an integrative methodology, combining both molecular microbial ecology and water geochemical data. The bioremediation potential of CEs was evaluated in two contaminated sites, presenting both dichloroethene (DCE) and vinyl chloride (VC) accumulation. These aquifers were investigated using multivariate statistics applied to data matrix combining environmental variables, bacterial community structures determined by terminal-restriction fragment length polymorphism and detection of dechlorinating bacteria and genes by specific PCR. The multifactorial analysis of data obtained from 25 groundwater samples from a PCE-contaminated site in Switzerland showed that manganese reduction (MR) was a key terminal electron accepting process, suggesting a potential competition between MR and DCE degradation to VC. Ethene was detected in low concentrations as well as Dehalococcoides sp. and VC reductive dehalogenase genes. Therefore, the potential for the complete biodegradation of PCE was present in this aquifer. However, the reduction of DCE will be strongly inhibited under the local conditions as long as oxidized manganese resources are present. The second site (Velamos, Czech Republic) sampled at 7 different dates making a total of 35 groundwater samples, was under active biostimulation process. Statistical analysis of the environmental parameters showed that successive cheese whey injections modified the aquifer conditions, becoming favourable for the complete dechlorination, and also for sulfate reduction (SR) and methanogenesis. However, DCE and VC accumulated along with the production of ethene, methane and hydrogen sulphide. This indicated a competition between CEs dechlorination and SR and methanogenesis, and possibly explained a transitional slower reaction of CEs dechlorination during the remediation process. Bacterial populations correlated with ethene production were related to Geobacter sp. and Dehalococcoides sp. In conclusion, statistical analysis combining the whole environmental and bacterial data allows evaluation of the bioremediation potential present in contaminated aquifers and elucidating mechanisms responsible for the incomplete dechlorination of CEs.