In order to investigate the reactive-transport patterns of nitrate in hyporheic zone during the hyporheic exchange process under a dynamic water level condition, a vertical two-dimensional numerical model of riverbed dune including (river) water fluctuations and sinuous river bed dune was constructed. By considering three types of river level fluctuations scenarios, river bed slope, aerobic respiration, nitrification and denitrification processes in our model, the effects of bed slope and water level fluctuatio scenarios on spatiotemporal evolution of solute distribution and nitrate conversion efficiency of hyporheic zone were systematically discussed. The results show that larger river bed slope condition can increase the solute exchange flux between surface water and the groundwater flow, and reduce the variation degree of solute concentration, which will consequently decrease the conversion efficiency of NO₃ ^‒ in hyporheic zones. Larger subsequent peak level of water fluctuations can prolong hyporheic flow path and increase the variation degree of solute concentration, whereas it can reduce the conversion efficiency of NO₃ ^‒ in hyporheic zones. The duration of subsequent water level fluctuations will affect the time response of solute concentration, but will not affect the conversion efficiency of NO₃ ^‒. Different delay times of subsequent water level fluctuations will affect the humber of NO₃ ^‒ concentration peaks. Furthermore, longer delay time can result in multiple peaks of NO₃ ^- concentration.