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The Salt River is an important urban river in Kaohsiung, Taiwan. In this study, the source identification and risk and toxicity assessment of the heavy‐metal‐contaminated sediments in the Salt River were investigated. The geo‐accumulation index (Igeo), enrichment factor (EF), sediment quality guidelines (SQGs), potential ecological risk index (RI), pollution load index (PLI), and toxic units (TU) were applied to determine effects of heavy metals on microbial diversities and ecosystems. Results from the ecological and environmental risk assessment show that high concentrations of Zn, Cr, and Ni were detected in the midstream area and the sum of toxic units (ΣTUs) in the midstream (7.2–32.0) is higher than in the downstream (14.0–19.7) and upstream (9.2–17.1). It could be because of the continuous inputs of heavy‐metal‐contained wastewaters from adjacent industrial parks. Results also inferred that the detected heavy metals in the upstream residential and commercial areas were possibly caused by nearby vehicle emissions, non‐point source pollution, and domestic wastewater discharges. Results of metagenomic assays show that the sediments contained significant microbial diversities. Metal‐tolerant bacterial phyla (Proteobacteria: 24.4%–46.4%, Bacteroidetes: 1.3%–14.8%, and Actinobacteria: 2.3%–11.1%) and pathogenic bacterial phyla (Chlamydiae: 0.5%–37.6% and Chloroflexi: 5.8%–7.2%) with relatively high abundance were detected. Metal‐tolerant bacteria would adsorb metals and cause the increased metal concentrations in sediments. Results indicate that the bacterial composition in sediment environments was affected by anthropogenic pollution and human activities and the heavy‐metal‐polluted ecosystem caused the variations in bacterial communities. Practitioner Points: Microbial community in sediments is highly affected by heavy metal pollution.Wastewaters and vehicle traffic contribute to river sediments pollution by heavy metals.Proteobacteria, Bacteroidota, and Actinobacteria are dominant heavy‐metal‐tolerant bacterial phyla in sediments.Toxicity assessment is required to study risk levels of heavy‐metal contained sediments. [ABSTRACT FROM AUTHOR]