The long-term industrialization and urbanization of Guangzhou city may lead to heavy metal contamination of its aquatic sediment. Nevertheless, only few studies have been published on the distribution and contamination assessment of heavy metals in this urban river sediment. Thus, the major objective of this study was to quantitatively assess contamination of heavy metals and their chemical partitioning in the sediments of the Guangzhou section of the Pearl River (GSPR). Surface sediment samples were collected at 10 sites in the main river and 12 sites in the creeks of the GSPR. The total content of Cd was determined by graphite furnace atomic adsorption spectrometry (GF-AAS), and content of Cr, Cu, Pb and Zn was determined by inductively coupled plasma atomic emission spectrometry (ICP-AES). The chemical partitioning of these heavy metals in the sediments of the main river was determined by the sequential selective extraction (SSE) method. Results indicated that the average total concentrations of Cd, Cr, Pb, Cu and Zn in the sediments of the main river were 1.44, 63.7, 95.5, 253.6 and 370.0 mg/kg, respectively, whereas they were 2.10, 125.5, 110.1, 433.7 and 401.9 mg/kg in the sediments of the creeks. The sediment at M4 and C9 sites was heavily contaminated with about 8 and 11 of toxic unit, respectively. Cr, Cu, Pb and Zn were mostly bound to organic matter and in the residual phase, whereas Cd was mostly associated with the soluble and exchangeable phase and the residual phase. The mobility and bioavailability of Cd, Zn and Cr in the sediments of the main river were relatively higher than Cu and Pb, due to higher levels in the soluble and exchangeable fraction and the carbonate fraction. The potential acute toxicity in the sediments of the main river and creeks was mainly caused by Cu contamination, accounting for 21.7-37.1% and 16.9-46.3% of the total toxicity, respectively, followed by Zn and Pb. Adverse biological effects induced by heavy metals would be expected in the sediments of the GSPR. Therefore, the sediments of the GSPR, especially at M4 and C9 sites, need to be remediated to maintain aquatic ecosystem health.