Abstract Bed form celerity, the migration rate of ripples along a sediment bed, has previously been shown to have dramatic effects on oxygen distribution and transport within the hyporheic zone of permeable sediments. This has the potential to influence denitrification rates—in particular by increasing the coupling of nitrification and denitrification. To further understand this, we numerically modeled nitrogen cycling under migrating ripples. While the simulated oxygen profiles match with expected behavior, almost no effect on denitrification or coupled nitrification‐denitrification was observed with increasing celerity. Instead, denitrification rates were dominantly controlled by the flow velocity of water overlying the sediment.