Understanding the transport of biochar and heavy metals is important for evaluation of the long-term stability and ecotoxicity of heavy metals after biochar remediation. In this study, 13C-labelled biochar was prepared to investigate the synergistic down migration of biochar and heavy metals in the soil profile, and the effect of ionic strength (IS) and flow rate was examined. Results showed that the 13C-labelled biochar with high δ13C (249.3 ‰) was suitable for tracing the migration of biochar without influencing its adsorption for heavy metals (i.e., Cu2+ and Cd2+). Both higher IS and flow rate were favorable for the release of biochar, but higher IS inhibited the transport of biochar in soil profile, which was attributed to the enhanced primary- and secondary-minimum deposition based on the Derjaguin–Landau–Verwey–Overbeek (DLVO) analysis. The transport of Cu2+ and Cd2+ was facilitated by high IS and flow rate. The release of Cd from biochar was mainly affected by IS, due to ion exchange and a weaker electrostatic attraction to biochar at higher IS, while that of Cu was mainly affected by flow rate related to co-migration of metal with biochar. Metal-biochar particle was the dominant form to migrate in upper soil layer, whereas, soluble Cd2+ and Cu2+ desorbed from biochar were the dominant forms that migrated to the deeper soil. The synergistic down migration of biochar and heavy metals might pose less risks than the sole migration of soluble metals. That is, high IS might cause higher risks than high flow rate even though biochar and metals might transport further with high flow rate. These findings will advance the current knowledge on the migration risk involved in the in-situ remediation of heavy metal-contaminated soils by biochar.