Abstract Understanding the transport of point source solutes across the sediment–water interface (SWI) is important for the protection of river environments. Conventional coupled models assume the porous media layer as Darcy's laminar flow and therefore cannot accurately capture the transport processes within the porous media. Furthermore, the effect of the porous structure of the riverbed on the transport process is largely unknown. In this study, we performed pore-scale numerical simulations of point source solutes transport across the SWI to investigate the effects of different porous structures in the riverbed on flow and point source dispersion. By solving the Reynolds-averaged Navier–Stokes equations with the k–ω shear stress transport turbulence closure model, we determine the complex flow field information and the spatial distribution of point source solutes for the coupled model. The results indicate that the presence of porous structures creates recirculation zones in the coupled model, which prevents turbulent structures reaching deeper layers. Random porous structures induce more preferential flow, inhibit the formation of recirculation zones, and exhibit higher solute dispersion, which is directly related to turbulent solute fluxes. Furthermore, our study reveals that the release position of point sources significantly influences the distribution of solute concentrations within the porous bed.