At a field site in the industrial area of Vilvoorde, Belgium, we investigated the capacity of the indigenous microbial community of a eutrophic river sediment to biodegrade chlorinated aliphatic hydrocarbons (CAHs) originating from discharging, polluted groundwater using a compound-specific isotope approach. We specifically targeted the site's major pollutants cis-1,2-dichloroethene (cis-DCE) and vinyl chloride (VC). Analysis of Rayleigh correlation plots enabled us to assess the extent to which microbial and abiotic natural attenuation processes contributed to the mitigation of a pollution of the surface water due to discharging CAH-contaminated groundwater. Our results provide evidence for (i) the occurrence of biodegradation of cis-DCE and VC by reductive dechlorination in parts of the aquifer and at several positions in the river sediment (ii) the presence of river sediment zones exhibiting attenuation of chloroethenes by a combination of biodegradation and dilution through unpolluted water, (iii) the existence of zones in the river sediment lacking significant biodegradation, and thus (iv) a pronounced spatial heterogeneity in the occurrence and extent of biodegradation in the aquifer and river sediment. We conclude that at many investigated positions in the river sediment the indigenous microbial community failed to facilitate complete biodegradation of the groundwater-sourced chloroethenes. The overall intrinsic bioremediation capacity of the river sediment was thus not high enough to completely prevent the release of these pollutants into the surface water. These findings and conclusions are thus in agreement with those of our companion paper (1), which investigated the river sediments at the Vilvoorde study site by a combination of stable hydrogen and oxygen isotope analysis of water and the detection of chlorinated aliphatic hydrocarbons (CAHs) and their dechlorination products.