Abstract This study aims to investigate the process and mechanism of adsorption of Zn(II) and Pb(II) by river sediments under hydrodynamic conditions. Surface sediments were collected from the Ganjiang River in Nanchang, China, and the adsorption characteristics of heavy metals Zn(II) and Pb(II) under different hydrodynamic conditions were simulated using the particle entrainment simulator. The results showed that under different hydrodynamic conditions, the adsorption equilibrium of Zn(II) and Pb(II) can be reached within 6h, and the adsorption amount of Pb(II) by the sediment was significantly higher than that of Zn(II). Pseudo-second-order dynamics and the Elovich model can better describe the kinetics of adsorption in both metals (R2 > 0.90). The Langmuir model and Freundlich model could better simulate the adsorption isotherms of Zn(II) and Pb(II) on sediments, which revealed that the adsorption spots are heterogeneous. According to the △G and −F results the adsorption of Zn(II) and Pb(II) is mainly physical adsorption. Furthermore, there are certain differences in the adsorption of heavy metals Zn(II) and Pb(II) by sediments at different pH, where the adsorption amount of Zn(II) increases with the increase of pH, but Pb(II) is not sensitive to the change of pH.