AbstractBenthic oxygen dynamics and the exchange of oxygen and other solutes across the sediment‐water interface play a key role for the oxygen budget of many limnic and shallow marine systems. The sediment‐water fluxes are largely determined by two factors: sediment biogeochemistry and the thickness of the diffusive boundary layer that is determined by near‐bottom turbulence. Here, we present a fully coupled benthic‐pelagic modeling system that takes these processes and their interaction into account, focusing especially on the modulation of the sediment‐water fluxes by the effects of near‐bottom turbulence and stratification. We discuss the special numerical methods required to guarantee positivity and mass conservation across the sediment‐water interface in the presence of rapid element transformation, and apply this modeling system to a number of idealized scenarios. Our process‐oriented simulations show that near‐bottom turbulence provides a crucial control on the sediment‐water fluxes, the oxygen penetration depth, and the re‐oxidation of reduced compounds diffusing upward from the deeper benthic layers especially on time scales of a few days, characterizing oceanic tides, internal seiching motions in lakes, and mesoscale atmospheric variability. Our results also show that the response of benthic‐pelagic fluxes to rapid changes in the forcing conditions (e.g., storm events) can only be understood with a fully coupled modeling approach.