Abstract Sequential extraction technique was used to study the mobility and dynamics of operationally determined chemical forms of heavy metals in the sediments and their ecological risk on the biotic species. The results reveal that high environmental risk of Cd, Ni, Co and Pb, are due to their higher availability in the exchangeable fraction. Substantial amount of Cd, Co, Mn, Cu, Zn, Ni and Pb, is observed as carbonate bound, which may result due to their special affinity towards carbonate and their co-precipitation with its minerals. Colloids of Fe–Mn oxides act as efficient scavengers for the heavy metals like Zn, Pb, Cu, Cr, Co, and Ni. Toxic metals like Ni, Pb and Cd are of concern, which occasionally may be associated with adverse biological effects based on the comparison with sediment quality guidelines (SQGs). The risk assessment code (RAC) suggests that the highest mobility of Cd poses a higher environmental risk and also threat to the aquatic biota. Factor analysis reveals that the enrichment of heavy metals in bioavailable fraction is mostly contributed from anthropogenic sources. These contributing sources are highlighted by cluster analysis.