Abstract: Reclaimed water has been widely used to restore rivers and lakes in water scarce areas. The hyporheic layer, which is an important interface between the surface of the water and groundwater, is an active ecotone in a river ecosystem. In order to figure out the distribution of temperature and flow field of hyporheic layer in riparian zones under the influence of temperature water, a real-time monitoring of water temperature and water level was conducted from September 2013 to January 2014. The temporal and spatial variation of temperature in the hyporheic layer is analyzed in this study. The corresponding influencing factors are also discussed. Three different methods are used to calculate groundwater flow rate, including Hatch phase method, Hatch amplitude method and hydrodynamic method, respectively. The results of the calculation via different methods are compared and discussed. The results show that ground temperature of vadose zone increases gradually with the increase in soil depth, and it varies dramatically with time. Air temperature and water contents are the major factors affecting vadose zone temperature in the hyporheic layer. Groundwater temperature decreases with increased depth, and it changes gently with time. The variation trend of groundwater temperature with depth is different from that in the vadose zone temperature. The groundwater flow rate ranges from 6.34 to 8.36×10^-5 m/s, 0.61 to 1.01×10^-5 m/s and 6.74 to 7.74×10^-5 m/s during the observation period, according to the Hatch phase method, Hatch amplitude method and hydrodynamic method, respectively.Compared to hydrodynamic method, groundwater flow rate obtained from the Hatch phase method and Hatch amplitude method shows a lag in time. Among three methods, the Hatch phase method has the highest accuracy. The results also show that the groundwater flow rate decreases with depth. For three different methods, the variations of groundwater flow rate show a similar trend. The study on hyporheic zones and hyporheic exchange mechanism will impose significant effects on assessing the development and utilization of water resources, and on maintaining and restoring the health of a river ecosystem.