The bottom feeding fish species have a good potential to be used for assessments of pollution, as they are under pressure from pollutants from both water and sediments. In this study, the level of similarity of histopathological responses to pollution in gills and liver between barbel (Barbus barbus) and sterlet (Acipenser ruthenus) from the Danube River was assessed, and compared with elemental concentrations in their gills, liver, and muscle. Results indicate that the detected metal concentrations were likely cause of different tissue responses in gills and liver of the two investigated fish species. Statistical analysis indicated a clear differentiation of the two species based on elemental concentrations and the level of histopathological changes in gills and liver. Metal concentrations exceeded maximum acceptable concentrations in a number of analyzed specimens, which indicates the importance of this type of monitoring. Results indicate that barbel is a better indicator for specific, rather narrow sites, whereas sterlet is a better indicator of larger (longer) water current segments. Obtained information could be of importance for both scientists and fishery and water management authorities working on the development of water monitoring programs. © 2014 Wiley Periodicals, Inc. Environ Toxicol 30: 1153–1161, 2015.