The influence of bedform physical properties on the hyporheic exchange process was assessed by investigating the quantitative correlation and variation between the permeability of bedform elements and hyporheic exchange flux. This investigation was conducted using laboratory annular flume experiments and conceptual two-dimensional discrete bedforms. Based on the results, it was observed that bedform permeability has a significant impact on the hyporheic exchange process. Within the bounds of the experimental parameters, the presence of bedforms was found to introduce an additional pumping exchange. The contribution of this pumping exchange to the overall hyporheic exchange flux was found to be closely related to the permeability variation in the bedform elements. When the permeability of these elements was low, the pumping exchange and turbulence penetration decreased, leading to an overall reduction in the effective diffusion coefficient when compared to scenarios with a flat bed.