The Lattice-Boltzmann (LB) method is applied here for the first time to simulate bedform-induced hyporheic exchange flow in a reduced complexity model. The flexibility of the LB allows surface and hyporheic flows to be resolved together, in contrast to other approaches for similar model domains, in which surface flow is usually solved independently, and then the solution of the surface flow provides the boundary conditions to model the hyporheic exchange flow. At the same time, the superior computational efficiency of LB allows the use of Large Eddy Simulations within transient simulations. Numerical results show a faithful reproduction of pressure along the bedform surface—especially, the pressure drop leeward to the dune. Results also show short-time-dependent phenomena which were previously described only in the context of DNS studies over reduced-size computational domains. Short-time-dependent phenomena include pressure oscillations and time-dependence of hyporheic zone morphology, with the latter eventually extending beyond the limits of a single bedform element.