Metal contaminants from surface water pollution events often enter hyporheic zones, under certain conditions, they may be released back into streams, causing secondary pollution to the water quality. The present study investigated the effects of adsorption, permeability, and anisotropy of sediment beds on the release of zinc ions (Zn2+) from the hyporheic zone into overlying turbulent flows using large-eddy simulations (LES). The volume-averaged Navier-Stokes equations and advection-diffusion equation with adsorption term were used to describe the sediment in-flow, adsorption, and convective diffusion of Zn2+ within the sediment layer. The effects of sediment permeability on the Zn2+ concentration distribution and mass transfer processes were investigated by time-averaged statistics of flow and concentration fields. The results show that adsorption becomes stronger as the pH value increases, leading to a slow increase in Zn2+ concentration in the overlying water layer and reaching a lower steady-state concentration. Higher overall permeability of the sediment layer can enhance mass and momentum exchange near the sediment-water interface (SWI), and intensify the release of Zn2+ from the sediment layer into the overlying water. As the wall-normal permeability of the sediment layer increases, the normal turbulent intensity strengthens, momentum transport enhances the wall-normal Zn2+ concentration flux increases, the effective diffusion coefficient increases, and the concentration in the overlying water increases.