Chlorinated ethenes, frequently encountered contaminants in groundwater, are often found to be incompletely dechlorinated to dichloroethene and vinyl chloride, more toxic products that accumulate in the aquifer. Some of the concerns in designing remediation approaches based on biological dechlorination are i) the presence of bacteria capable of completely reducing chlorinated ethenes, and ii) the competition events for available electron donors between classical biogeochemical processes and the reductive dechlorination process. For this purpose, an assessment methodology was developed to explore the existing relations between autochthonous bacterial communities, degradation state of chlorinated ethenes and redox processes, including reductive dechlorination. Three steps are involved with first the acquisition of abiotic environmental data, followed by assessing the biochemical potential for complete dechlorination and an analysis of bacterial community structures, and finally a statistical Multiple Factor Analysis combining datasets from geochemistry and microbiology. This approach was applied for diagnosing a Swiss aquifer for its in situ potential of complete reductive dechlorination, and for monitoring a Czech aquifer under bioremediation by successive cheese whey injections. The Swiss site contained the microbiological potential for complete dechlorination but the global redox conditions were not enough reducing and dichloroethene reduction was in competition locally with manganese reduction. The follow-up of the Czech site has shown that during the remediation process, complete reductive dechlorination was favored under sulfate-reducing conditions, but was in competition with other anaerobic bacterial processes leading to a transient accumulation of dichloroethene and vinyl chloride. In both cases, antagonist biogeochemical processes were identified as the reasons restricting the reductive dechlorination at the level of toxic intermediates. This approach is now formalized in a user-oriented manual, and could be integrated as tool for eligibility investigation of aquifers for a bioremediation strategy through natural attenuation.