A comparative study of the heavy metal (As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn) concentrations in sediments collected from the mainstream, tributaries, and lakes of the Yangtze River catchment of Wuhan, China, was conducted. Compared with the maximum background values in Wuhan Province soils, Cd was the metal with the highest contamination level, especially in the mainstream, followed by Zn and Cu. In a few samples from tributaries and lakes, the Hg concentration was very high compared to background levels. The concentrations of As and Ni in all sites fluctuated close to background levels. Partitioning of speciation of each heavy metal in sediments was similar for samples taken from the mainstream, tributaries, and lakes. Compared to the other metals studied, Cd, Cu, Zn, and Pb had higher bioavailability in the three zones, which means they pose a higher ecological risk. Significant correlations among group a (Zn, Cu, and Pb, r>0.9) and group b (Cr and Ni, r=0.978) in the mainstream; Hg, Cu, Cd, and Pb in lakes (r>0.9); and Cu and Pb (r>0.9) in tributaries were observed using Cluster and correlation analysis. However, a low correlation between As and the other elements in the three zones was shown. Overall, 63.6% of samples from the mainstream, 75.0% from tributaries, and 88.9% from lakes exhibited low and moderate ecological risk of heavy metals, and the potential ecological risks in the mainstream and tributaries were higher than those in lakes.