Hydrodynamic control of sediment-water fluxes: Consistent parameterization and impact in coupled benthic-pelagic models

Benthic 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 rapidchanges in the forcing conditions (e.g., storm events) can only be understood with a fully coupled modeling approach.