The Elbe River is one of the most polluted aquatic ecosystems in the Czech Republic. The effect of three major chemical plants located on the Elbe River (at Pardubice, Neratovice, and Usti nad Labem) on fish was studied in 2004. Health status, chemical concentrations (Hg, PCB, DDT, HCH, HCB, OCS, 4-tert-nonylphenols, 4-tert-octylphenol) in muscle, and biomarkers (hepatic ethoxyresorufin-O-deethylase (EROD), plasma vitellogenin, and plasma 11-ketotestosterone) were assessed in male chub (Leuciscus cephalus L.). Differences between localities upstream (US) and downstream (DS) from the monitored source of pollution were identified. Fish from DS sampling sites showed significantly higher levels of contaminants than fish from US sampling sites. Generally, the concentrations of pollutants in fish from the Elbe sites were significantly higher compared to the reference site. Reduced gonad size, decreased plasma levels of 11-ketotestosterone, EROD and vitellogenin induction, and histopathologies of male gonads indicated harmful effects of aquatic pollution in fish from the Czech portion of the Elbe River.