Widely used in industrial activities, chloroethenes have become common groundwater contaminants. Dehalorespiration is an anaerobic bacterial respiration coupling their sequential degradation to energy production. The interactions between the dehalorespiring bacteria and the other guilds and environmental variables are presumed to influence the dehalorespiration efficiency. Here, water and core samples were extracted from the PCE-contaminated site of Lyss (BE, Switzerland). Bacterial DNA was extracted and the 16S rRNA gene amplified by PCR. Terminal restriction fragment length polymorphism (T-RFLP) was used to assess the diversity of the bacterial communities. Core and groundwater environmental variables were analyzed as well. The T-RFLP profiles and the environmental data obtained were processed using statistical multivariate analysis. Within a period of two months, the bacterial communities remained relatively specific to their respective sampling origins. Communities from the oxic layer shared a similar set of bacterial species whereas piezometers from the anoxic layer had a specific one. The T-RFLP profiles obtained from single depth and multi-level piezometers were clearly distinct, probably due to differences in the pumping flow rates and their associated transport regimes, which can have an impact on i) the sediments extracted from the aquifer, ii) the hydraulic zone reached and iii) a potential selective bacterial adsorption onto the pumping tube wall. Environmental factors related to the groundwater redox state appeared as the major variables influencing the bacterial populations. Bacterial communities from core samples clustered into two distinct sets: i) samples from the strongly reductive silt layer, and ii) samples from the coarser and less reductive layer. Grain size distribution and redox state both had a major influence on the bacterial communities of core samples. Finally, it was shown that microbial populations extracted from groundwater differed from the ones extracted from core material, and thus were not representative of the overall aquifer microbial diversity.