Determining the distribution trends, transport mechanisms, and ecological risks of heavy metals (HMs) in urban river sediments is essential for the government to conduct appropriate remediation work. In this study, we collected sediment cores from the Yayao Waterway in Foshan City, China. The vertical distribution profiles of dissolved and labile Fe, Mn, Cd, Zn, Cu, Cr, Ni, Pb, As, and Co in the sediments were obtained using the thin-film diffusive gradient (DGT) and high-resolution peeper (HR-Peeper) techniques. In addition, the transport rates, contamination levels, and ecological concerns of the HMs were evaluated using the European Community Bureau of Reference (BCR) sequential extraction technique, the DGT-induced sediment fluxes (DIFS) model, and multiple contamination evaluation metrics. The results showed that most of the DGT-labile HMs were associated with Fe/Mn (hydrogen) oxides, and in particular, Zn, Ni, and Cr showed a significant negative correlation with Fe/Mn (p < 0.001). Additionally, Cd had the highest bioavailability (89.17%), and its net diffusive flux at the sediment–water interface (SWI) was positive, which indicated a high release risk from the sediment. However, the R-value of Cd based on the DGT-induced sediment fluxes (DIFS) operation was extremely low, suggesting that although Cd had the biggest supply pool of releases, its release rate was slow. The majority of sampling sites had significantly higher total HM contents in the surface sediments than the background values. The HM contamination in the sediments originated from human activities, primarily from industrial enterprises and with a large contribution from both agricultural and domestic sources. The most polluted HM with the highest ecological danger was Cd, followed by Cu, Zn, Ni, and As when the results of the four pollution evaluation indicators were combined. Consequently, the risk of contamination by HMs in inner-city river sediments should receive more attention.
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