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Abstract The seabed and the water column are tightly coupled in shallow coastal environments. Numerical models of seabed‐water interaction provide an alternative to observational studies that require concurrent measurements in both compartments, which are hard to obtain and rarely available. Here, we present a coupled model that includes water column biogeochemistry, seabed diagenesis, sediment transport and hydrodynamics. Our model includes realistic representations of biogeochemical reactions in both seabed and water column, and fluxes at their interface. The model was built on algorithms for seabed‐water exchange in the Regional Ocean Modeling System and expanded to include carbonate chemistry in seabed. The updated model was tested for two sites where benthic flux and porewater concentration measurements were available in the northern Gulf of Mexico hypoxic zone. The calibrated model reproduced the porewater concentration‐depth profiles and benthic fluxes of O₂, dissolved inorganic carbon (DIC), TAlk, NO₃and NH₄. We used the calibrated model to explore the role of benthic fluxes in acidifying bottom water during fair weather and resuspension periods. Under fair weather conditions, model results indicated that bio‐diffusion in sediment, labile material input and sediment porosity have a large control on the importance of benthic flux to bottom water acidification. During resuspension, the model indicated that bottom water acidification would be enhanced due to the sharp increase of the DIC/TAlk ratio of benthic fluxes. To conclude, our model reproduced the seabed‐water column exchange of biologically important solutes and can be used for quantifying the role of benthic fluxes in driving bottom water acidification over continental shelves. 

The Ayeyarwady and Thanlwin Rivers, which drain Myanmar, together form one of the largest point sources of freshwater and sediment to the global ocean. Combined, these rivers annually deliver an estimated 485 Mt of sediment to the northern Andaman Sea. This sediment contributes to a perennially muddy zone within the macro-tidal Gulf of Martaban, but little is known about the processes that dominate dispersal and trapping of sediment there, as very few water column observations are available. A research cruise in December 2017 provided a rare opportunity to obtain Acoustic Doppler Current Profiler (ADCP) data along transects from the Gulf of Martaban and adjacent continental shelf. Two transects were obtained from the outer portion of the Gulf of Martaban in water depths that ranged from about 20–35 m. These showed very fast currents, especially during flood tide conditions, exceeding 1.5 m/s. The backscatter record from the ADCP indicated asymmetries in distribution of suspended sediment during the ebb versus flood phase of the tide. During ebb tidal conditions, the backscatter record indicated that sediment was transported in either a surface advected layer, or fairly well-mixed throughout the water column. In contrast, during flood tidal conditions, sediment was confined to the bottom boundary layer, even though the velocities were faster during flood than the ebb conditions. The vertical structure of the currents during flood tide conditions indicated the presence of sediment–induced stratification because currents within the near-bed turbid layers were relatively slow, but speeds increased markedly above these layers. This albeit limited dataset provides an exciting glimpse into the dynamics of sediment transport within the muddy, macrotidal Gulf of Martaban, and implies the importance of tidal straining and bottom nepheloid layer formation there.