In order to evaluate the distribution and partitioning characteristics of heavy metals in the large anthropogenically impacted Pearl River Basin, the contents of “anthropophile” elements (Cr, Ni, Cu, Zn, Cd and Pb, which are clearly influenced by human activities) were determined, and their partitioning coefficients (K_d) between water and sediments and enrichment factors (EF) were calculated for samples collected at different locations along the Pearl River main stream. The modified BCR sequential extraction procedure (proposed by the European Community Bureau of Reference in 1993), which involves the successive extraction of metals in a decreasing order of reactivity, was applied. Sediment samples from the upper, middle, and lower reaches were included in this study. The results showed that the content of most metals in water and sediment samples gradually increases from upstream to downstream, suggesting a possible input from human activities as shown by their increasing high EF, ranged from 1.4 to 3.9 for Cu, from 1.4 to 6.7 for Zn, from 2.5 to 59.1 for Cd, and from 1.7 to 8.9 for Pb, respectively. The higher partition coefficients (K_d) for Cr, Zn, and Pb (10⁵–10⁶) indicated that they were mainly transported in solid phase, while parts of Ni, Cu, and Cd were transported in dissolved phase as they display relatively lower K_d in the range of 10⁴–10⁵. According to the results of the BCR leaching, the percentage of non-residual fraction of heavy metals in the sediments showed a decreasing order of Cd > Pb > Zn > Cu > Ni > Cr, implying that Cd and Pb were more active and bioavailable compared to the other four metals, and thus would be potentially more harmful to the watershed ecosystem.