The microbiological impact of zero-valent iron remediation of groundwater was investigated by exposing a trichloroethylene-degrading anaerobic microbial community to bare and coated iron nanoparticles. Changes in population numbers and metabolic activity were analyzed using qPCR and were compared to those of a blank, negative, and positive control to assess for microbial toxicity. Additionally, these results were compared to those of samples exposed to an equal concentration of iron filings in an attempt to discern the source of toxicity. Statistical analysis revealed that the three iron treatments were equally toxic to total Bacteria and Archaea populations, as compared with the controls. Therefore, toxicity appears to result either from the release of iron ions and the generation of reactive oxygen species, or from alteration of the redox system and the disruption of microbial metabolisms. There does not appear to be a unique nanoparticle-based toxicity.