Based on the monitoring of five heavy metal elements in the surface sediments of the Pearl River in South China, potential toxicity of the heavy metals was assessed using consensus-based sediment quality guidelines (SQGs) method and geo-accumulation (I(geo)) index method. The monitoring results showed the heavy metal concentrations were significantly and positively correlated with each other, demonstrating a common trend in variation of concentration in the surface sediments. The assessment using the consensus-based SQGs method showed the potential toxicity of Cu was the highest, and Cd was the lowest. The evaluation based on mean probable effect concentration (PEC) quotient showed the region was seriously polluted with high toxicity heavy metals. Correlation analysis revealed a significant and positive correlation between the mean PEC quotient and the average of I(geo) with a correlation coefficient of 0.926 (n = 23, P < 0.01). In conclusion, the consensus-based SQGs and mean PEC quotient are applicable to assess potential toxicity risks of heavy metals in freshwater sediments in the Pearl River.