Integrated source analysis and risk assessment of metals facilitate the development of targeted risk management strategies. However, previous studies usually addressed total concentration rather than bioavailability, and consequently overestimated metal risk, especially natural source-related risk. In this study, a source-specific risk assessment was conducted by integrating the source analysis of bioavailable metals in surface sediments. Moreover, risk assessment was performed using two bioavailability-based indices: the total availability risk index (TARI) and a modified index of mean probable effect concentration quotients (mPEC-Q). A representative river watershed in eastern China was selected as the study area. Findings revealed that the total concentrations of Pb, Cu, Zn, Cr, and Ni in the sediments were 1.4–2.2 times higher than the local soil background values. Using a modified community bureau of reference (BCR) sequential extraction procedure, the dominant fraction for Pb, Cu, Zn, and Cr in the studied area was found to be the residual fraction, constituting 53.63–62.44% of the total concentrations. This suggested that a significant portion of the metals potentially originated from natural sources. Nevertheless, the concentration enrichment ratio (CER) indicated that anthropogenic sources contributed significantly, accounting for 67.84–87.68% of bioavailable metals. The positive matrix factorization (PMF) model further identified three different sources of bioavailable metals, with a descending concentration contribution sequence of industrial sources (37.61%), mixed traffic and natural sources (33.17%), and agricultural sources (29.22%). Both the TARI and mPEC-Q index values indicated that the bioavailable metals generally posed a moderate risk, and Ni was the priority pollutant. Industrial sources contributed the most to the total risk, although the contribution from TARI-based assessment (37.27%) was lower than that from the mPEC-Q assessment (46.43%). This study provides an example of the consideration of metal bioavailability in the context of source-specific risk assessments to develop more reasonable management strategies.