Abstract: The surface sediments collected from major lakes located in Guangzhou City were analyzed for the concentration and spatial distribution of Cd, Cr, Cu, Ni, Pb and Zn. The pollution and potential ecological risk of which were assessed using the methods of geo-accumulation index, enrichment coefficient and potential ecological risk index. The results show that the concentrations of Cd, Cr, Cu, Ni, Pb, and Zn were 0.50-6.90, 36.00-197.40, 32.35-432.00, 17.35-155.50, 32.50-162.70, 71.83-853.40 mg·kg^-1, with average of 2.54, 92.27, 165.20, 70.21, 90.48, 447.88 mg·kg^-1, respectively, being significantly higher than those of background values in soils of Guangdong Province. As for spatial variation, the concentrations of heavy metals were higher in Baiyun Lake and Dongshan Lake than those of Liuhua Lake and Huadu Lake. Based on geo-accumulation index and enrichment coefficient, that the heavy metals pollution followed the order of Cd > Cu > Zn > Ni > Pb > Cr. According to the potential ecological risk factor, Cd was identified as the key ecological risk factor and the result indicate that Baiyun Lake and Dongshan Lake met the extreme serious ecological risk, Liuhua Lake and Huadu Lake fall at the level of serious ecological risk. Multivariate statistical analysis indicate that the heavy metals in lakes of Guangzhou City were mainly derived from the runoff of city, and direct and indirect discharge of industrial and domestic sewage.