Lateral Mixing Processes in an Estuary: San Francisco Bay and its Exchange With Perimeter Habitat

Observations from the South San Francisco Bay are presented to examine lateral mixing processes in an estuary. Irregularities in the shoreline lead to lateral density gradients that are set up by tidal trapping, which disrupts the phasing of flows and scalar concentrations along the estuary's axis. In South San Francisco Bay, thousands of acres of salt ponds are being breached to the Bay's influence for the first time in decades as part of a landscape-scale salt marsh restoration project. The tides deliver salt, sediment, and nutrients to the subsided ponds, aggrading their surfaces and converting them to marsh. These newly inter-tidal ponds around the perimeter of the South San Francisco Bay constitute a highly irregular shoreline, capable of initiating steep, periodic lateral density gradients. In this study, we focus on a small cluster of salt ponds and the tidal slough to which they were breached. The exchange between the tidal slough and the ponds is representative of the larger estuary, but of a spatial scale small enough that we can conduct field experiments to examine the flows and transport of scalars in detail. We conducted two boat-mounted transecting surveys of the tidal slough in June and July of 2008, during which we collected profiles of velocity with a down-looking 1200 kHz ADCP, continuous CTD measurements of surface water temperature and salinity, and discrete CTD profiles of salinity and temperature. We have observed that water and salt are trapped in the ponds on the flood tide, and released on the ebb out of phase with the slough's primary salinity gradient. Additionally, the momentum of the ebbing flow in the channel confines the pond effluent to the near bank just down-estuary of the breach. This leads to the coincidence of two distinct water masses, and a sharp change in salinity of 3 PSU over a distance less than 10 meters. We use our data to construct detailed velocity and density fields across and along the tidal slough as the lateral salinity gradients are induced and relaxed. We then explore the resulting periodic, buoyancy-driven cross-sectional mixing, and its implications for estuarine transport on two time and spatial scales: first, the cross-sectional mixing affects shear dispersion, which influences the tidally averaged, longitudinal flux of salt and other scalars, such as suspended sediment. Second, the variability of buoyancy-driven mixing within the tidal cycle affects the quantity of salt and sediment delivered to habitat areas, as well as the grain size distribution and source of sediment transported.