A two-year survey on the water quality characteristics of Aliakmon river in northern Greece is described. Heavy metals (Pb, Cd, Cr, Cu, Mn and Fe) were determined in the dissolved fraction, as well as in two particulate fractions, labile and residual, separated after a two-step sequential extraction procedure. The partitioning of metals between different fractions was examined at various sampling sites along the river. Variations observed were related to the geology of the transected area and the influence from anthropogenic sources (mainly municipal effluents). Statistical analysis of variance of metal partition coefficient showed significant differences between sampling periods, while insignificant ones between sampling sites. Factor analysis of analytical data yielded four factors that were interpreted as natural, anthropogenic, geological and run-off contributions.