ABSTRACT We investigated the contents and distributions of nutrients and heavy metals in sediment from the Yitong River. The main aims were to analyze heavy metals speciation and evaluate their bioavailability, in order to assess the risks they pose to both ecosystem and human health. The average total nitrogen (TN), total phosphorus (TP), organic matter (OM) and Cd, Cr, Cu, Ni, Pb and Zn contents were 1747.69, 895.58, 75103, 0.19, 75.64, 33.61, 47.17, 56.65 and 159.91 mg kg−1, respectively. Results from acid-extraction fraction analysis showed that the proportions of Cd and Zn ranged from 3.78% to 30.20% and 5.31% to 30.74%, respectively. Health risk assessment model showed the risk index values of children and adults were 0.412 and 0.059, respectively, indicating a minimal threat to human health. Multivariate statistical analyses revealed that TN and TP may have similar sources and could be attributed to combined sewer overflows, while Cr, Cu, Ni and Zn were primarily derived from industrial pollution sources. Toxicity bioassay tests demonstrated that the majority of sediment samples were classified as non-toxic. However, 25% of the samples showed slight toxicity towards Vibrio qinghaiensis Q67, while 7% of the samples exhibited slight toxicity towards Daphnia magna. Based on these findings, it is necessary to implement pollution control measures and conduct assessments of aquatic ecological risks in sediments from urban rivers. These results can be used to develop effective strategies for the management and governance of aquatic sediments.