This paper summarizes a 4-year survey focused on polycyclic aromatic hydrocarbons (PAHs) and halogenated persistent organic pollutants (POPs) in river sediments, soil and crops collected in the locality impacted by catastrophic floods that occurred in the western part of Bohemia in August 2002. In spite of relatively high levels of polychlorinated biphenyls (PCBs) in river sediments, the increase of these POPs in flooded arable soil was not significant. On the other hand, remarkably higher levels of PAHs and dichlorodiphenyl trichloroethane (DDTs) were found as compared to those in reference soil samples. Regardless of this increased soil pollution, no measurable elevated concentrations of POPs occurred in the wheat grown in this area.