River sediments are a major source of metal contamination in aquatic food webs. Due to the ability of metals to move up the food chain, fishes, occupying higher trophic levels, are considered to be good environmental indicators of metal pollution. The aim of this study was to analyze the metal content in tissues of the common barbel (Barbus barbus), a rheophilous cyprinid fish widely distributed in the Danube Basin, in order to find out if it can be used as a bioindicator of the metal content in the river sediment. We analyzed bioavailable concentrations of 15 elements (Al, As, B, Ba, Co, Cr, Cu, Hg, Mn, Mo, Ni, Pb, Se, Sr, and Zn) in sediments of the Danube (D), the Zapadna Morava (ZM), and the Južna Morava (JM) using the inductively coupled plasma spectroscopy (ICP-OES). The barbel specimens were collected in the proximity of sediment sampling sites for the analysis of metals in four tissues, gills, muscle, intestine, and liver. The sediment analysis indicated that the ZM is the most polluted with Cu, Ni, and Zn compared to other two rivers. The JM had the lowest concentrations of almost all observed elements, while the Danube sediments were mainly characterized by higher concentrations of Pb. The fish from the ZM had the highest concentration of Cu and Ni in the liver and intestine, and of Zn in the muscle tissue, which was in accordance with the concentrations of these metals in the sediment. Scanning electron microscopy/energy dispersive X-ray spectroscopy (SEM-EDS) was used for further analyses of metal interactions with fish tissues. The results suggest that the barbel can potentially be used as a bioindicator of sediment quality with respect to metal contamination.