Ports and rivers adjacent to the coast often suffer from high siltation rates. In order to maintain water depths of ports and rivers sediment needs to be frequently dredged. In many cases this sediment is polluted and dumped elsewhere in the water system. The Elbe estuary represents the largest and economically most important German estuary. Due to changed hydrodynamics the siltation rates increased in the past years. In consequence 6mio m³ low polluted sediment was dredged and dumped in the German Bight since 2005. The dumping activity is subject to severe governmental restrictions as biannual monitoring programs to observe the impact on benthic organisms and fishes. To today the impact of ocean dumping on benthic microbial communities is not included in these monitoring programs. Microbial communities represent the basis of any ecosystem. Substantial functions as nutrient cycling might be affected by changes in community structure and composition. In a pilot study we investigated microbial communities in three monitoring campaigns in August 2009, April and August 2010. Each campaign comprised 125 sampling stations at the dumping area including the dumping site and a reference site. We utilised automated ribosomal intergenic spacer analysis to obtain profiles of microbial communities of each sampling station. Microbial communities’ information was linked to contextual data as grain size fractions and pollutants. Additionally, representative samples were chosen to yield phylogenetic information by 454 pyrosequencing. Microbial communities of the reference site and dumping site remained significant different in all sampling campaigns. After a dumping activity we observed significant different microbial communities at the dumping site. Redundancy analyses revealed a strong gradient of grain size distributions and pollutants affecting the microbial community structure. Finally 454 sequencing revealed a unique microbial community at the dumping centre. The presence of sulphate-reducing groups affiliated to Deltaproteobacteria, especially Desulfuromonadaceae and Desulfobacteraceae appeared to be affected by the dumped material. In conclusion our results suggest a significant impact of the dumping activity on benthic microbial communities. Its consequences need to be clarified urgently. We suggest the inclusion and elaboration of microbial community analyses in future monitoring programs in order to verify anthropogenic impacts on ecosystems.