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.