The flow of bottom water across sediment topographies such as ripples is an important driver of porewater flow in permeable shelf sediments and is well studied using laboratory flumes and mathematical models. However, most of these studies assume steady state conditions and neglect the dynamic interaction between bottom water currents and sediment topography. As such, sediment redistribution (ripple formation and migration), introduces another mode of porewater exchange and leads to a dynamic change of porewater flow. To study these interactions we applied a multi-physics model coupling the transport in bottom water (Large-Eddy-Simulation) and porous media (Darcy) with rates of oxygen respiration. Ripple migration was implemented using additional transport terms in the porous domain. Migrating ripples significantly changed the oxygen distribution as oxic porewater formation at the lee side of the ripple increased and O2 inflow at the stoss side was hindered. At high migration velocities, ripples became fully oxic and strongly separated from underlying anoxic layers. The results indicate that morphodynamics significantly increase the spatio-temporal variability of redox conditions to which micro-organisms are exposed in permeable sediments.