Abstract: The hyporheic zone is the key transition region between rivers and aquifers, which is highly dynamic and sensitive. Frequent water exchange can trigger the bio-geochemical reactions within the hyporheic zone easily, and consequently make a difference to river ecological security. On the purpose of improving the authenticity and validity of the hyporheic flow hydrodynamic monitoring, the present study introduces various monitoring methods including seepage, water pressure, solute & temperature tracing and their applicability, and summarizes the monitoring points arrangement in the riverbed and adjacent riparian zone and the data acquisition frequency of different monitoring methods. The hyporheic exchange theory and calculation methods for reach, riverbed and riparian zone are summarized systematically, and the factors causing measurement uncertainties of the hyporheic exchange are discussed in the paper. In view of the deficiencies of the existing monitoring methods and the development direction of future research, it is proposed to strengthen the application of multi-method joint and multi-technology integration in future and carry out the lateral hyporheic flow monitoring and uncertainty analysis. By this means, the reliable data for studies on the coupling mechanism between hydrological and bio-geochemical processes in the hyporheic zone might be provided.