The extreme flooding of the Elbe in August 2002 led to resuspension of large amounts of sediment and thus to elevated loads of organic substance in the river. The higher organic carbon concentration was only slightly balanced by increased microbiological self‐purification capability, and this led to regional organic pollution along the river Elbe, especially in lentic water bodies. The remobilisation of sediments also led to increases in the concentrations of some elements by a factor of more than three times. In October 2002, the concentrations of most elements decreased to their 1998 values with the exception of As, Cd, W, Bi and U. One year after the flood an algae bloom and biogenous decalcification led to increases in organic matter and calcite in the suspended matter and sediments and therefore to dilution of most of the elements. However, the concentrations of Cd, W and Bi in the 2002 and 2003 sediments were higher than in 1998.