Bacteria of marine sediments play a crucial role in carbon and nutrient cycles. Surprisingly little is known about the natural succession and the response to environmental changes of benthic bacterial communities in the German Bight. As being very eclectic, the bacterial genome enables its carrier to adapt rapidly to these changes. Thus investigating the bacterial community allows following environmental changes, often caused by anthropogenic activities, very early. Waterways represent important connections in transport systems. Due to tidal pumping effects, sediment often accumulates in coastal rivers, inhibiting them. Dumping of these accumulations into the sea is a common procedure. But the impact of these potentially polluted sediments on bacterial communities of pristine environments is barely investigated. In this study the dumping site “Tonne E3” in the German Bight (North Sea, Germany) was examined. From 2005 to 2010 5 Mio m³ of excavated material from the Hamburg port area have been dumped into the North Sea. In 2009 and 2010 sediment samples were taken at “Tonne E3” to analyze the bacterial community via automated ribosomal intergenic spacer analysis (ARISA). The dumping area and a reference region were investigated. ARISA focuses on the highly conservative ITS region in the bacterial genome possessing a species specific length polymorphism. ARISA profiles of samples at the dumping area in 2009 and 2010 revealed different bacterial communities changing over time. The analyses of community data in conjunction with environmental data indicate sedimentological factors but also contaminants affecting the communities significantly. In 2009 highly heterogenic community patterns in the vicinity of the dumping area were observed. This interesting fact will be further investigated by performing 454 sequencing of the highly conserved 16S region for representative samples.