The concentrations and distributions of heavy metals Cu, Zn, Pb, Cd, Hg, and As in surface sediments were investigated with the samples collected from the Qiantang River. Then we analyzed the potential ecological risk of heavy metal with the Hakanson ecological risk index and searched for its source based on Pearson correlation coefficient and principal component analysis(PCA). Results showed that the concentrations of Cu, Zn, Pb, Cd, Hg and As in surface sediments of Qiantang River were rather high, the overall potential ecological risk level was extremely high. Cd and Hg were the prominent factors for ecological risks in surface sediments, showing the intensity of potential risk as extremely strong and strong, respectively. There was a certain distribution difference with different sections of the river, among which the concentrations and potential ecological risks in S3 section were both higher than others. It was likely that the sources of heavy metals in surface sediments were similar; industrial pollution, agricultural non-point source pollution, traffic pollution and domestic wastewater were the probable sources by the method of PCA. Besides, we determined the effects of heavy metal with surface sediment on fish in Qiantang River. Results showed that the biota-surface sediment accumulation factor(BSAF) of Hg was 0.861, which presented a bioaccumulation to fishes. However, the average levels of heavy metals in surface sediments presented low correlations with fish on overlying water samples. It may be caused by the fact that the water in Qiantang River flowed fast and the majority of fish investigated were from proliferation of releasing of young age.