It is important to understand heat transfer changes in the hyporheic zone of spur dikes when assessing ecological restoration and sustainability in rivers. To reveal the rule of hyporheic exchange under the action of a spur dike, the sinusoidal temperature change of surface water was set with a period of 24 h. The porous subsurface flow paths under different riverbed forms were plotted through dye tracing. In addition, the influences of surface water velocity (U), river width narrowing ratio (L/B), the number of spur dikes and riverbed shape on hyporheic exchange were also studied using the temperature tracing method. The results show that the hyporheic exchange path presents a trend of diagonal flow downstream, first conducting turbulent diffusion upstream and then sinking, with different riverbed morphologies having different path lengths. The temperature of surface water has a significant controlling effect on the temperature field of the riverbed. The sediment temperature change from the water–sediment interface to 0.3 m depth is closer to the sinusoidal trend. The change in surface water velocity (U) has the most significant effect on the temperature amplitude ratio. The temperature field below spur dikes is more susceptible to the impact of spur dikes and usually presents a “semielliptical” high-temperature area. With the increase in surface water velocity (U), river width narrowing ratio (L/B), and the number of spur dikes, the range of hyporheic exchange under the dam head also increases, which is positively related to the vertical section hyporheic exchange flux at the dam head. The local backwater area generated by spur dikes also affects pressure field distribution near spur dikes, but the changes caused by the fluctuation of the riverbed itself are greater than the impact of spur dikes on the riverbed. The water–sediment interface velocity at the spur dike increases sharply, and the upstream 1 m of the dam head gradually experiences upflow, drops sharply after reaching the maximum at the dam head, and then approaches zero after 1 m. There is no obvious upwelling and downwelling at the whole interface.
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