The distribution and extent of heavy metal accumulation in the fluvial sediment of the Beijiang River are described. The potential toxicity of this pollution was quantified using a consensus based sediment quality guidelines (SQGs) method and the Hakanson potential ecological risk index. The concentrations of Hg, As, Cu, Zn, Pb, Ni and Cr were high enough to damage the sediment biota on a frequent basis. The potential ecological risk was much higher in the downstream, urbanized reaches of the river than in the upstream reaches which are still rural, but all sections of the river posed at least a moderate level of ecological risk. Estimates of the economic loss associated with these pollutions were appreciable, and were mainly due to Hg and Cu. The Beijiang River basin is heavily polluted, posing environmental risks for the downstream reaches of the Pearl River, and economic loss to the whole watershed.