The Juru River flows through largely urbanized areas and is grossly polluted by domestic wastes and discharges from pig farms. Other than carrying highly polluting organic materials, these wastes are also contaminated with heavy metals. To ascertain the extent of heavy metal pollution in the river, total and non-residual concentrations of Cu, Pb, Zn, Mn and Fe in sediment samples collected along the river were determined. The results indicate that both the total and non-residual metal concentrations in sediments can successfully be used to identify heavy metal pollution sources. The speciation of Zn, Mn and Fe in the sediment samples were investigated using a sequential leaching technique which identifies the elements among six operationally defined host fractions: (1) exchangeable, (2) carbonate and surface-associated, (3) easily reducible, (4) moderately reducible, (5) bound to organic matter and sulphides and (6) residual. The results indicate that Zn is mainly associated with the reducible fractions. Zn and Fe found in the moderately reducible fraction are significantly correlated, indicating that iron oxides is the preferred host phase by Zn.