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Arsenic and antimony are widely distributed toxic metalloids in aquatic environments. However, their partitioning behaviors in the sediment profile remain not well understood. Here, partitioning behaviors, diffusive fluxes, as well as the ecological risks of As and Sb in the sediment–porewater profile system in the tributaries of the Three Gorges Reservoir (TGR) were investigated. As and Sb showed markedly different spatial variations in the longitudinal profiles of both porewater and sediment samples. Specifically, the concentration of As showed an accumulation trend with depth, while that of Sb showed a relatively complicated trend. Further, As showed lower sediment-porewater partitioning coefficient (K d) values, suggesting that it had a relatively lower sediment affinity and a higher mobility than Sb. Its residual fraction (30%–60%) was also lower than that of Sb. This phenomenon could be attributed to the chemical fractions of the trace metals and the pH value of the sediments. Furthermore, the K d values corresponding to As were influenced by both the residual fraction (r = 0.338, p < 0.05) and the exchangeable fraction (r = −0.643, p < 0.01), while those corresponding to Sb were only influenced by pH. Additionally, even though these two trace metals showed low ecological and mobility risks, the diffusive fluxes at the sediment-water interface suggested that the sediment acted as a source of As and a sink for Sb relative to the overlying water. This study indicated that As and Sb had different partitioning behaviors and release risks in the sediment–porewater profile system, enhanced the understanding the transport and fate of As and Sb in the aquatic environment. [Display omitted] • Partitioning behavior of As and Sb in the sediment-porewater profile was studied. • As and Sb showed different spatial variations in the longitudinal profiles. • Partitioning coefficient showed that Sb had a higher affinity and lower mobility than As. • Sediment acted as a source of As and a sink for Sb relative to the overlying water. [ABSTRACT FROM AUTHOR]