Longitudinal Versus Lateral Estuarine Dynamics and Their Role in Tidal Stratification Patterns in Lower South San Francisco Bay

The dynamics of shoal‐channel estuaries require consideration of lateral gradients and transport, which can create significant intratidal variability in stratification and circulation. When the shoal‐channel system is strongly coupled by tidal exchange with mudflats, marshes, or other habitats, the gradients driving intratidal stratification variations are expected to intensify. To examine this dynamic, hydrodynamic data were collected from 27 January 2017 to 10 February 2017 in Lower South San Francisco Bay, a small subembayment fringed by extensive shallow vegetated habitats. During this deployment, salinity variations were captured through instrumentation of six stations (arrayed longitudinally and laterally) allowing for mechanisms of stratification creation and destruction to be calculated directly and compared with observed time variability of stratification at the central station. We present observation‐based calculations of longitudinal straining, longitudinal advection, lateral straining, and lateral advection. The time dependence of stratification was observed directly and calculated by summing measured longitudinal and lateral mechanisms. We found that the stratification dynamics switch between being longitudinally dominated during the middle of ebb and flood tides to being laterally dominated during the tidal transitions. This variability is driven by the interplay between tidally variable lateral density gradients and turbulent mixing. Relatively constant along‐estuary density gradients are differentially advected during flood and ebb tides, resulting in maximal lateral density gradients around tidal transitions. Simultaneous decrease in turbulent mixing at slack tides allows lateral density‐driven exchange to stratify the estuary channel at the slack after flood. At the end of ebb, barotropic forcing drives negatively buoyant shoal waters toward the channel.Plain Language SummarySan Francisco Bay sits within a highly urbanized area. The dense population creates large wastewater effluent resulting in high nutrient levels. Scientists wonder why there have not been annual phytoplankton blooms like those observed in other estuaries with lower nutrient levels. Some have hypothesized it is due to high turbidity levels and tidal breakdown of stratification creating nonideal environments for phytoplankton growth. However, decadal trends show that the estuary is becoming less turbid, and with changes in climate patterns, there is potential for persistent stratification. We observed development of stratification over the ebb tide and destratification in two distinct events as the tide reverses over the flood tide. At the reversal of the tides, water in the shoals exchange with the water in the channel creating a pulse of salty water to the channel at the ebb to flood transition and a pulse of fresh water at the flood to the ebb transition. Destratification occurs in the early flood tide due to a pulse of saline water received from the shoals then due to the advection of less stratified water being pulled to the center channel of the estuary. Finally, stratification is destroyed completely due to longitudinal straining and turbulent mixing.Key PointsVertical stratification in shoal‐channel estuary is characterized by strong intratidal variabilityLateral circulation is a key driver of intratidal stratification dynamics at tide transitionsTiming and magnitude of longitudinal straining, advection, lateral straining, and advection set intratidal vertical stratification dynamicsPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151865/1/jgrc23594_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151865/2/jgrc23594.pd

Perimeter exchange, hydrodynamics, and scalar transport in an estuary

The exchange of flow and scalars between an estuary and its perimeter controls the hydrodynamics in the estuary's fringes as well as along its axis. The flow and scalar fields in these two regions are coupled through tidally-driven lateral exchange. The physical processes that regulate this exchange operate on tidal timescales (hours, days) and respond to perturbations such as meteorological events and morphologic changes. The long-term, or residual, effects of this system of processes define the physical and ecological functioning of an estuary by controlling its morphology, salt field, and distribution of flows. In this dissertation research, field observations and theoretical analysis are used to explore the influence of an estuary's exchange with its perimeter on flow and scalar fields at tidal and residual timescales. In-situ measurements of flow velocity and water properties were collected in a macrotidal slough in the South San Francisco Bay lined by mudflats and recently connected to former salt ponds.The interplay between tidal flows, bathymetry, and the longitudinal salt gradient define the pattern of stratification and mixing during a tidal cycle. The mechanism of tidal straining combined with the longitudinal baroclinic pressure gradient typically work together to enhance stratification on ebb tides and break it down through active mixing on flood tides. In the presence of sharp bathymetric transitions, such as the shoal-channel interface, the typical dynamics can be overwhelmed by local exchange. On flood tides, baroclinically-driven lateral circulation between the channel and mudflats freshens the surface layer in the channel, and reduces its velocity, producing a sub-surface velocity maximum. The input of buoyancy and the velocity shear result in stable stratification. On ebb tides, outflow from the mudflats transports trapped, high-salinity water over the freshening bottom layer, producing strong lateral shear and unstable stratification near the channel-mudflat boundary. As the ebb tide progresses and the mudflat outflow decelerates, the water column becomes well-mixed, and exhibits increased turbulent motions that result from shear and buoyant production. In short, lateral exchange in this tidal channel has reversed the classical pattern of stratification at the mudflat-channel boundary.The transport of suspended sediment through an estuary is determined by an intricate system of physical, biological, and chemical processes. The physical transport dynamics are sometimes described by a balance of particle settling and turbulent resuspension, but in a tidal channel that exchanges with a complex perimeter, this balance is overly simple. Along the channel's axis, resuspension is the main mechanism elevating suspended sediment concentrations on the flood, and particle settling reduces concentrations when slack tide arrives. On the ebb, horizontal advection results in quickly recovering concentrations of sediment before turbulent stresses increase enough to suspend material from the bed. Tidal asymmetries reflect the role of the settling and scour lags, and make this balance an unsteady one where the net transport is landward. The tidal asymmetry reverses and increases in magnitude in response to wet weather as newly deposited material works its way down-estuary on successive ebb tides. In the presence of irregular bathymetry, such as near the channel-mudflat boundary and inside a breached salt pond, much of the sediment deposited in the shallows cannot be resuspended on the ebb due to strong friction opposing tidal forcing, resulting in net deposition. The combination of low concentrations of suspended sediment in the shallows on ebb tides with bathymetrically generated shear in local velocities produces the periodic occurrence of high sediment concentrations near the water surface and low concentrations near the bed. This establishes the importance of the role of lateral advection on ebb tides. The presence of complex bathymetry therefore requires that horizontal advection and unsteadiness be accounted for when describing the mechanisms driving transport of suspended sediment.Understanding dispersion of scalars, such as salt and sediment, in an estuary over long timescales is critical for estuarine physics as well as managing the influence of humans on the environment. An irregular shoreline and accompanying bathymetry result in tidal trapping, a dispersive mechanism that arises from differences in phasing of flow velocities and scalar concentrations between the estuary's axis and its perimeter, as well as the variations in mixing between these regions. Classical theories describing the residual effects of tidal trapping assume that exchange between the estuary and perimeter is diffusive, but this framework neglects the role of tidal advection, such as the filling and draining of side-embayments, and the branching of flows into channel networks. A new theoretical framework is developed to represent estuarine dispersion from tidal trapping driven by advective exchange. The new advective framework compares well to observations