UC Berkeley

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 was collected from January 27, 2017 ‐ February 10, 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 6 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 towards the channel.

Plain Language Summary

San 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 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.