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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 salinity structure in an estuary is controlled by time‐dependent mixing processes. However, the locations and temporal variability of where significant mixing occurs is not well‐understood. Here we utilize a tracer variance approach to demonstrate the spatial and temporal structure of salinity mixing in the Hudson River Estuary. We run a 4‐month hydrodynamic simulation of the tides, currents, and salinity that captures the spring‐neap tidal variability as well as wind‐driven and freshwater flow events. On a spring‐neap time scale, salinity variance dissipation (mixing) occurs predominantly during the transition from neap to spring tides. On a tidal time scale, 60% of the salinity variance dissipation occurs during ebb tides and 40% during flood tides. Spatially, mixing during ebbs occurs primarily where lateral bottom salinity fronts intersect the bed at the transition from the main channel to adjacent shoals. During ebbs, these lateral fronts form seaward of constrictions located at multiple locations along the estuary. During floods, mixing is generated by a shear layer elevated in the water column at the top of the mixed bottom boundary layer, where variations in the along channel density gradients locally enhance the baroclinic pressure gradient leading to stronger vertical shear and more mixing. For both ebb and flood, the mixing occurs at the location of overlap of strong vertical stratification and eddy diffusivity, not at the maximum of either of those quantities. This understanding lends a new insight to the spatial and time dependence of the estuarine salinity structure.