Geochemical behaviors of trace metals in the sediment profiles are crucial for predicting the associated environmental risks in aquatic ecosystems. However, the comprehensive transport of trace metals under both equilibrium and dynamic conditions is still unclear under the changing hydrological regime. Here, the equilibrium partitioning behaviors and remobilization of five trace metals (Ni, Cu, Zn, As, and Pb) in sedimentary profiles within the tributaries of the Three Gorges Reservoir were explored by the partitioning coefficient (Kd), diffusive gradients in thin films (DGT), and DGT induced flux in sediments (DIFS) model. According to the Kd values, As posed the highest migration ability among the trace metals in the sediment profiles under equilibrium circumstances. Similarly, the dynamic processes of trace metals simulated by the DIFS model also suggested that As displayed the highest desorption rate despite having the lowest labile pool size. Moreover, all trace metals were classified as the “partially sustained” case, while the supply abilities of As and other trace metals were limited by the diffusion and the desorption kinetics, respectively. In addition, DGT-labile trace metals showed a diffusion trend from the sediment to the water column (except for Zn) at the sediment-water interface, indicating potential risks to water quality. Specifically, the equilibrium partitioning behaviors revealed the potential labile pool of trace metals in the solid phase, and the dynamic resupply process between the solid phase and porewater remained undetermined. In comparison, although DGT simulated the kinetic process of trace metals in the sediments, the labile pool of the trace metals could not be obtained. This study provided a holistic insight into the complementary trace metal behaviors under both equilibrium and dynamic conditions in the sediment and was beneficial to the water quality protection and internal pollution remediation in the aquatic environment.