This study investigated the influence of the regional flow on the streambed vertical hydraulic conductivity (Kv) within the hyporheic zone in three stream reaches of the Weihe River in July 2016. The streambed Kv with two connected depths was investigated at each test reach. Based on the sediment characteristics, the three test reaches could be divided into three categories: a sandy streambed without continuous silt and clay layer, a sandy streambed with continuous silt and clay layer, and a silt–clay streambed. The results demonstrate that the streambed Kv mainly decreases with the depth at the sandy streambed (without continuous silt and clay layer) and increases with the depth at the other two test reaches. At the sandy streambed (with continuous silt and clay layer) where streambed Kv mainly decreases with the depth, the regional upward flux can suspend fine particles and enhance the pore spacing, resulting in the elevated Kv in the upper sediment layers. At another sandy streambed, the continuous silt and clay layer is the main factor that influences the vertical distribution of fine particles and streambed Kv. An increase in streambed Kv with the depth at the silt/clay streambed is attributed to the regional downward movement of water within the sediments that may lead to more fine particles deposited in the pores in the upper sediment layers. The streambed Kv is very close to the bank in the sandy streambed without continuous silt and clay layer and the channel centre in the other two test reaches. Differences in grain size distribution of the sediments at each test reach exercise a strong controlling influence on the streambed Kv. This study promotes the understanding of dynamics influencing the interactions between groundwater and surface water and provides guidelines to scientific water resources management for rivers.