The evaluation of resident fi sh communities is an important component of the ecological status assessment in aquatic habitats. Despite signifi cant water quality improvement in the Czech Republic in the last decade, several important pollution sources in the Elbe River basin remain. The aim of the study was to evaluate fish community in a chronically polluted part of the channelized lowland Elbe River and its potential indicative capability. The effluent from both industrial and municipal sewage treatment plant exhibited low pH, high conductivity and wide set of organic compounds (PAH, PCB, DDT etc.). Ecological characteristics of fi sh communities were obtained by boat electro fishing at selected sites in four inter-weir sections in July 2005 and 2006. Relatively high fish species richness (24 species) was observed in both seasons. Generalists (bleak, roach, chub) form the majority of the fish community in all four sections. There was no significant difference in fish species richness or density among study sections (river segments between weirs) even with a high level of measured organic compounds at the pollution inlet. Signifi cant differences in fish species richness and density were registered among individual sites within study sections. Sites downstream the weirs had signifi cantly higher species richness and density than the other two sites in the middle and upstream weirs. Fish community does not display any indicative remarks concerning water pollution, or in the case of mid-size river, sampling strategy was not effi cient to recognize it. Channelization and regulation of the study stretch of the Elbe River seems to be the most important determinant of fi sh community structure.