Abstract Heavy metals contamination in freshwater ecosystems has drawn attention worldwide. It is necessary to investigate heavy metals content and assess their ecological risk in order to protect the aquatic ecosystems. In this study, we collected surface sediment samples from the freshwater ecosystem of the city of Zhenjiang, in China, in both winter and summer. Then, we analyzed the seasonal and spatial distribution patterns of lead (Pb), chromium (Cr), cadmium (Cd), zinc (Zn), and copper (Cu). The contamination factor (CF), enrichment factor (EF), geo-accumulation index (I_geo), and potential ecological risk (E_rⁱ) were jointly used to assess the pollution degree and the ecological risk posed to the freshwater ecosystem by the aforementioned elements. Multivariate statistical analysis, including Pearson’s correlation and principal component analysis and cluster analysis, were used to identify potential sources of the investigated metals in this research area. Study results showed that: (1) the average concentrations values were 1.81 mg/kg and 1.15 mg/kg for Cd, 55.3 mg/kg and 62.2 mg/kg for Cu, 88.0 mg/kg and 52.5 mg/kg for Cr, 27.3 mg/kg and 22.8 mg/kg for Pb, 87.0 mg/kg and 271 mg/kg for Zn, in winter and summer, respectively. Amongst the investigated elements, the average concentrations of Cd, Cu, Cr, and Pb, were above the local background values in winter, whereas, Cd, Cu and Zn concentrations were higher than the background values in Zhenjiang; (2) The CF and EF indicated that Cd had a high contamination degree and a significant enrichment compare to others investigated metals in the surface sediment of in this research area. (3) Cd posed moderate, considerable, or very high ecological risks in different sites, while the other elements (i.e., Cu, Cr, Pb, and Zn) presented a low degree of ecological risk. (4) Multivariate statistical analyses results indicated Pb, Cu, and Zn had similar geochemical characteristics, while, Cd and Cr had significant differences with the above elements. Therefore, Pb, Cu, and Zn probably originate from the same sources, while Cd and Cr might have mixed sources, including both natural sources and human activities. Overall, more attention should be paid to Cd for risk assessment in the current study area. The findings of this study provide fundamental information for the evaluation and management of the heavy metals investigated in the freshwater ecosystem of Zhenjiang.