In August 2002 extreme floods affected Bohemia a part of the Czech Republic, along Vltava and Labe rivers. After the flood had culminated, soil samples of arable and meadow soil (flooded and control-non-flooded) have been collected in the surroundings of the cities of Ceske Budejovice (CB, South Bohemia, the Vltava river, the upper flood stream) and Usti nad Labem (UL, the Labe river, the lower flood stream). Different parameters of arable soils have been affected more significantly than those of meadow soils. Soil texture e.g. has been shifted from sandy loam to loam (CB) and clay loam (UL). Organic carbon, total phosphorus and nitrogen contents have been increased as well as the content of some hazardous elements such as arsenic. A shift of soil pH from 6.1 to 4.8 has been noticed in CB and an opposite one from 5.1 to 7.1 was measured in UL. Available phosphorus decreased in CB by 56% while a four-fold increase was measured in UL. Chlorinated organic pesticides level was significantly reduced, but that of polycyclic aromatic hydrocarbons (PAH) increased up to the maximum values of legal limits. The UL arable soil also became heavily contaminated by PAH. The CB arable soil demonstrated high microbial activity, while UL arable soil suffered under stress conditions in this respect. The flooded meadow soils became covered with a layer of drifted soil sediment, which retained enhanced content of the PAH’s different hazardous elements, and, in addition, the soil aeration was reduced