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The hyporheic zone (HZ) is a saturated sediment layer connecting groundwater (GW) and surface water (SW) along a riverbed and river channel. The HZ plays an important role in connecting SW and GW in a river ecosystem, thereby helping maintain the ecological health of rivers. Studies on the HZ have therefore increased in many disciplines. This study used the VFLUX 2 software to assess vertical fluid flux in the HZ, in which the Hatch, Kerry, McCallum, and Luce models were applied and compared. The simulations were calibrated against data measured by the US Geological Survey at a water diversion channel within the Walker River Basin in Nevada. Using COMSOL Multiphysics, we developed a two-dimensional coupled numerical model of the saturated seepage and temperature fields, calibrated against measured temperature data. We also determined the vertical seepage velocity and compared the simulations with those of the analytical models in VFLUX 2. The results showed that the temperature field distribution of the HZ is obviously nonuniform in space. With a deeper monitoring point, the thermal response of each temperature measurement pointed to periodic temperature fluctuations of the SW, which exhibited attenuation and hysteresis characteristics. When the vertical flow velocity of GW was sufficiently large, an error in the accuracy of the Kerry model amplitude ratio was observed, regardless of the heat dispersion coefficient used. Under conditions of local GW recharge by SW and a heterogeneous permeability coefficient, the use of the amplitude ratio method is recommended to quantify the vertical GW flow rate in the HZ. [ABSTRACT FROM AUTHOR]