Although flood events are natural events, they may have an impact on the condition of a river system, i.e. when polluted deposits are involved in the process. The quality of the transported matter is mainly affected by the origin of the flooding water as well as the remobilization of deposits within the catchment area (e.g., groyne fields, lock-and-weir systems, mining and industrial areas, sewage plants). Transport and fate of a contaminant in the water body are significantly influenced by the ratio of the concentrations in the dissolved and the particulate phase. Depending on their morphology, floodplains act as sink for suspended matter (Engelhardt et al. 1999; Friese et al. 2000; Hanisch et al. 2005; Costa et al. 2006). In the Middle Elbe groyne fields are the characteristic morphological feature. The resuspension of deposited, not yet consolidated groyne field sediments can lead to the first SPM (suspended particulate matter) peak in the course of a flood, a long time before the flood crest has arrived (Spott and Guhr 1996; Baborowski et al. 2004). All further peaks are the result of matter flow and inputs further upstream of the location, e.g., tributary inflows. Therefore the remobilization processes in groyne fields upstream of a sampling location play the most important role for the right starting time of a flood sampling campaign (Baborowski et al. 2005). The assessment of sediment dynamic and pollutant mobility in rivers requires the integration of various experimental and modeling techniques (Förstner et al. 2000; Förstner 2004). They have to include aspects of erosion (Gust and Muller 1997; McNeal et al. 1996; Haag et al. 2001), transport (Brunk et al. 1997) and deposition (Asselmann and Middelkoop 1995; Kronvang et al. 2002; Krüger et al. 2006). In the paper results of investigations on transport and deposition in the middle part of the river Elbe are presented.