In‐stream wood structures, such as single logs, river steps, and debris dams, are known to drive hyporheic flow, defined as the flow that goes into the subsurface region and then back to the free‐flowing surface water. The hyporheic flow plays an important role in regulating water quality and biogeochemical cycles in rivers. Here, we investigated the impact of a channel‐spanning porous log jam, representing piles of wood logs, on hyporheic flow through a combination of direct visualization and theories. Specifically, we developed a method using refractive index‐matched sediment to directly visualize the hyporheic flow around and below a porous log jam, formed by piles of cylindrical rods, in a laboratory flume. We tracked the velocity of a fluorescent dye moving through the transparent sediment underneath the log jam. In addition, we measured the water surface profile and the spatially varying flow velocity near the log jam. Our results show that the normalized log jam‐induced hyporheic flux remained smaller than 10% at Froude numbers () below 0.06 and increased by a factor of five with increasing at . We combined the mass and momentum conservation equations of surface flow with Darcy's equation to explain the dependency of the log jam‐induced hyporheic flux on . Further, we observed that at , the water surface dropped noticeably and the turbulent kinetic energy increased immediately on the downstream side of the log jam. These findings will facilitate future quantification of hyporheic flow caused by channel‐spanning porous log jams.