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The SAFIRA in situ pilot plant in Bitterfeld, Saxonia-Anhalt, Germany, currently serves as the test site for eight different in situ approaches to remediate anoxic chlorobenzene (CB)-contaminated ground water. Two reactors, both filled with original lignite-containing aquifer material, are designed for the microbiological in situ remediation of the ground water by the indigenous microbial consortia. In this study, the hydrogeological, chemical and microbiological conditions of the inflowing ground water and reactor filling material are presented, in order to establish the scientific basis for the start of the bioremediation process itself. The reactors were put into operation in June 1999. In the following, inflow CB concentrations in the ground water varied between 22 and 33 mg L−1; a chemical steady state for CB in both reactors was reached after 210 till 260 days operation time. The sediments were colonized by high numbers of aerobic, iron-reducing and denitrifying bacteria, as determined after 244 and 285 days of operation time. Furthermore, aerobic CB-degrading bacteria were detected in all reactor zones. Comparative sequence analysis of 16S rDNA gene clone libraries suggest the dominance of Proteobacteria (Comamonadaceae, Alcaligenaceae, Gallionella group, Acidithiobacillus) and members of the class of low G+C gram-positive bacteria in the reactor sediments. In the inflowing ground water, sequences with phylogenetic affiliation to sulfate-reducing bacteria and sequences not affiliated with the known phyla of Bacteria, were found.