Chlorinated ethenes (CEs), such as perchloroethene (PCE) and trichloroethene, are one of the most common classes of groundwater contaminants. In this project, the contaminant biodegradation capacities of two aquifers, presenting both dichloroethene (DCE) and vinyl chloride (VC) accumulation, was carried out. Aquifers are considered nowadays as dynamic ecosystems, showing multiple interactions between the physical, chemical and biotic components. In this sense, an integrative methodology using multivariate statistics and combining together bacterial community structures, detection of dechlorinating bacteria and genes, and water geochemical data were used to investigate these aquifers. Results from multifactorial analysis of data collected from a PCE-contaminated site in Switzerland (25 groundwater samples) showed that manganese reduction (MR) was a key terminal electron accepting process, suggesting a potential competition between MR and DCE degradation to VC and ethene. Dehalococcoides sp. and VC reductive dehalogenase genes were detected but ethene concentration was below 0.007mg/L. Potential for a complete natural biodegradation of PCE was present in this aquifer. However, DCE reduction is strongly inhibited under local conditions as long as oxidized manganese resources are present. The second site located in Czech Republic (Velamos) and sampled at 7 different dates (35 groundwater samples) was under an active biostimulation process. Multifactorial analysis showed that successive cheese whey injections modified the aquifer habitat that became favourable not only for a complete dechlorination, but also for sulfate reduction (SR) and methanogenesis. DCE and VC accumulated along with the production of ethene, methane and hydrogen sulphide, indicating a competition between CEs dechlorination and SR and methanogenesis. This possibly explained the transitional slower reaction of CEs dechlorination observed during the remediation process. In conclusion, the used methodology allowed evaluation of the bioremediation potential present in contaminated aquifers and monitoring biostimulation processes.