Large amounts of toxic metals are discharged into rivers and lakes, but little is known about the factors that drive the adsorption and transformation of these metals in the hyporheic zone and the exchange flux across the sediment-water interface. To better understand transport and transformation of metal ions in the hyporheic zone, flume experiments and numerical simulations were performed in a streambed with periodic bedforms using zinc ions. Compared to non-adsorbing contaminant, the results show that adsorption leads to a more rapid decrease in the concentration of Zn2+ in the overlying water, and a lower final concentration is reached. The mass of adsorbed ions is several times higher than that of free ions in the bedform’s water phase. Indeed, metal adsorption is in the shallow layer of the streambed. Although this prevents heavy metal groundwater contamination, the same cannot be said of shallow layer of the hyporheic zone. Knowledge of the migration and transformation of metal ions in the hyporheic zone provides insights pertinent to the restoration of polluted rivers.