Numerous industries have been using chloroethenes (CEs), mainly tetrachloroethene and trichloroethene, as non-flammable solvents since the beginning of the 20th century. Massive usage, along with careless handling and storage, made CEs one of the most abundant classes of aquifer contaminants. Porous aquifers are dynamic ecosystems showing complex interactions between physical, chemical and biotic components. These environments are inherently extremely heterogeneous in their structure and composition, even at very small scale, in terms of lithological composition, grain size distribution and chemical composition, and thus provide a large variety of living conditions. However, to date only few studies have been focusing on the influence of the aquifer properties on the total bacterial communities in such habitats. Here, we assessed the influence of environmental factors on the microbial communities present in a CE-contaminated aquifer. Both grain size distribution and geochemical composition showed low correlations with the bacterial community structures. In this aquifer, a very slow groundwater flow combined with a restricted aquifer recharge probably limited the nutrients availability. These limitations were hypothesized to be the main factors driving the apparent structures observed for the communities involved in the reductive dechlorination of the contaminants.