Anthropogenic activities such as mining, smelting industries, and the application of pesticides in agriculture might re-sult in contamination of multiple heavy metals in the environment. Heavy metal contamination of sediment is a serious environmental problem, and thus the remediation of contaminated sediment is a worldwide challenge. Several strat-egies have been developed for the remediation of contaminated sediment, however the ecological risk and ecotoxicity of the restored sediment have rarely been evaluated. We assessed whether river sediment highly contaminated with heavy metals could be restored using microbial bioleaching followed by evaluating the residual toxicity and ecological risk of the microbially remediated sediment. Sequential extraction revealed that the bioavailable levels of Cu, Ni, and Zn in the contaminated sediment exceeded sediment quality guideline (SQG) thresholds. It was consequently found that acidophilic sulfur-oxidizing Acidicaldus sp. SV5 effectively bioleached Cu, Ni, and Zn from the contaminated sed-iment, reducing the bioavailable fraction of these elements below SQG thresholds. The ecological risk assessment in-dicated that SV5-driven remediation significantly reduced the potential ecological risk of the contaminated sediment. The residual ecotoxicity of the microbially remediated sediment was also tested with the soil nematode Caenorhabditis elegans. There was a significant decrease in the body burden of Cu, Ni, and Zn in C. elegans and a reduction in the tox-icological effect on survival, growth, and reproduction in the microbially remediated sediment. Our study suggests that a combination of chemical analysis, chemical-based ecological risk assessment, and ecotoxicity tests would be helpful for the development of efficient and eco-friendly strategies for the restoration of contaminated sediment, which could be incorporated into sediment quality management practices.