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In the course of this study 37 sediment samples were analyzed. They were taken after the flooding in September 2002 along the Elbe and at the mouths of its major tributaries. The sampling program covered the entire river stretch that was affected by the floods, from Obristvi (Czech Republic) to the Elbe estuary (North Sea) on the German coast. Analyses were performed for dioxins, nonylphenols, nonylphenol ethoxylates, bisphenol A, DEHP, musk fragrances, polybrominated diphenylethers, chloroalkylphosphates, organochlorine compounds, PAH, and organotin compounds. The results show that only a few weeks after the flood, contaminant concentrations in solid matter were comparable to those prevailing beforehand. Significant sources of contaminant input proved to be the tributaries Vltava (Moldau), Bilina (both in the Czech Republic), and the Mulde (Germany), as well as industrial and municipal sewage treatment works (STW) located along the Elbe. Further point sources are to be found in still water zones such as harbors and abandoned channels. These sources are activated when erosive action stirs up older sediments. Statistical analyses of the congener distribution of the dioxins provided evidence on the sources of these contaminants and freight levels in different river sections. The chemical analyses were complemented by results of ecotoxicological investigations with two sediment organisms (Chironomus riparius and Potamopyrgus antipodarum).