Cellular changes in livers from flounder (Platichthys flesus L.) and digestive glands of blue mussels (Mytilus edulis) were studied to analyze whether the Elbe flood catastrophe in August 2002 had any deleterious effects on animal health. Flatfish and mussels were sampled at different locations in the Elbe estuary and the Wadden Sea after the flood wave had reached the German Bight. Internationally used core biomarkers (lysosomal membrane stability, biotransformation enzymes) were applied to assess the toxic effects of putatively increased pollution levels. In comparison to earlier data from long-term studies at the same stations, we found a significant impairment in the function of cell organelles (lysosomes) involved in the detoxification and elimination of pollutants in fish liver. Concentrations of relevant contaminants (organochlorines, polychlorinated biphenyls) were analyzed in parallel with cellular biomarkers, and conspicuously raised concentrations of insecticides metabolites were detected. Cell recovery and a clear reduction in contaminant concentrations were observed in fish livers five months after the flood at all sampling sites except the Helgolander Tiefe Rinne.