In the present study, concentrations of heavy metals (Cd, Cu, Co, Mn, Cr, Ni, Pb, and Zn) were determined at 35 river sediments in Serbia. The anthropogenic heavy metals input and quantification of the metal enrichment degree in sediments were estimated by calculating geo-accumulation indices (I(geo)) and enrichment factors (EF). These pollution indices have been calculated using different background values (continental crust and local background values) and different element used for normalization (Al and Fe), followed by result comparison. The EF values calculated with continental crust as background (minor to extremely severe enrichment) were higher than when regional background values were used (minor to moderate enrichment). Significant influence of background values on the I(geo) values is observed. Values of geo-accumulation index (<2) revealed that studied river sediments are remaining unpolluted to moderately polluted with Co, Mn, Cr, and Ni. Significant pollution in the sediments was observed for Cd, Cu, Pb, and Zn elements. The results of this study confirm the relevance of precise and accurate determining of local background concentrations while assessing sediment pollution. The values of EFs for studied elements were more influenced by the choice of background values than selection of element used for normalization. Our recommendation would be to use the local and regional background content in quantification of metal contamination in sediments, since these values differ and are site and region dependent.