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Abstract Estuarine exchange flow controls the salt balance and regulates biogeochemistry in an estuary. The Albemarle‐Pamlico estuarine system (APES) is the largest coastal lagoon in the U.S. and historically susceptible to a series of environmental issues including salt water intrusion and eutrophication, yet its estuarine exchange flow is poorly understood. Here, we investigate the estuarine exchange flow in the APES, its tributary estuaries (Pamlico and Neuse), and sub‐basin Albemarle Sound using the total exchange flow analysis framework based on results from a deterministic numerical model. We find the following: (a) Dynamics controlling estuarine exchange flow in the APES vary spatially and depend on timescales considered. At inlets, estuarine exchange flows respond to both tidal prism and residual water levels at weather‐to‐spring/neap timescales. At a long quasi‐steady timescale represented as annual means, estuarine exchange flow is dominated by barotropic flow. Within the tributary estuaries, estuarine exchange flows at timescales of wind periods are controlled by wind‐induced straining, whereas the quasi‐steady state condition is dominated by gravitational circulation. At Albemarle Sound, exchange flow is dominated by the residual water levels at weather‐to‐spring/neap timescales, while at quasi‐steady state it is controlled by barotropic flow. (b) At the quasi‐steady annual timescale, the salt content decreases with river discharge. At the weather‐to‐spring/neap timescales, salt content is insensitive to variations in estuarine exchange flow, except for within Albemarle Sound. (c) Estuarine exchange flow likely influences the biogeochemistry of the APES by playing a key role in regulating the flushing efficiency and material exchange, a role that has been previously overlooked. 

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. 

Abstract Extreme precipitation during Hurricane Florence, which made landfall in North Carolina in September 2018, led to breaches of hog waste lagoons, coal ash pits, and wastewater facilities. In the weeks following the storm, freshwater discharge carried pollutants, sediment, organic matter, and debris to the coastal ocean, contributing to beach closures, algae blooms, hypoxia, and other ecosystem impacts. Here, the ocean pathways of land‐sourced contaminants following Hurricane Florence are investigated using the Regional Ocean Modeling System (ROMS) with a river point source with fixed water properties from a hydrologic model (WRF‐Hydro) of the Cape Fear River Basin, North Carolina's largest watershed. Patterns of contaminant transport in the coastal ocean are quantified with a finite duration tracer release based on observed flooding of agricultural and industrial facilities. A suite of synthetic events also was simulated to investigate the sensitivity of the river plume transport pathways to river discharge and wind direction. The simulated Hurricane Florence discharge event led to westward (downcoast) transport of contaminants in a coastal current, along with intermittent storage and release of material in an offshore (bulge) or eastward (upcoast) region near the river mouth, modulated by alternating upwelling and downwelling winds. The river plume patterns led to a delayed onset and long duration of contaminants affecting beaches 100 km to the west, days to weeks after the storm. Maps of the onset and duration of hypothetical water quality hazards for a range of weather conditions may provide guidance to managers on the timing of swimming/shellfishing advisories and water quality sampling.