Inorganic and organic pollutants (nutrients and toxic pollutants) are liable to accumulate in suspended and bottom sediments. The major transport of these pollutants takes place in the suspended load. Sedimentation and resuspension are in dynamic equilibrium along the river influenced mainly by physical processes.

International and national surveys on the Danube sediment concluded that the Danube reach between Vienna and Budapest is one of the most polluted ones in addition to the Irongate reservoir and the downstream reach. The main polluting compounds are petroleum hydrocarbons, including PAHs, and heavy metals. Reservoirs are the major traps of sediment-bound pollutants where pollutant “time-bombs” may be developed.

Pollutant monitoring of the bottom sediment requires careful selection of the representative sampling sites where the sediment contains at least 10 percent clay and silt which is enriched in pollutants. Mobilization of the sediment-bound pollutants will result in biological uptake by the benthic organisms. The macrozoobenthons monitoring provides valuable evidence for chronic biological stress associated with contaminated sites. Benthic biodiversity decreased along the studied Danube reach downstream of recognized hot spots such as major cities (Vienna, Bratislava, Budapest) and polluted tributaries (the Vah river, etc.). Harmonization between chemical measurements and biological observations in the sediment could eventually lead to an effective Danube pollution monitoring system.