Transport and accumulation of large amounts of natural and man-made substances takes place in the Odra River. The river is a significant source of pollution for the Baltic Sea. The presence of toluene in the samples of benthic sediments collected after the flood in 1997 was an unexpected find made within the framework of the International Odra Project (IOP). At that time, the origin of toluene, which is a pollutant characteristic of benthic sediments, was not elucidated. Variation in toluene concentrations along the course of the river suggested that the compound might have been of microbial origin. The aim of this study was to find the source of toluene identified in samples of benthic sediments in the Odra River basin after the 1997 flood.