UC San Diego

Many estuaries in the Mediterranean climate of Southern California are low-inflow estuaries (LIEs), where minimal freshwater input only intermittently drives the buoyancy gradient. LIEs therefore have circulation structures and ecological communities distinct from classical estuaries, and face stressors including mouth closure from sill buildup, and slow flushing pollution. This dissertation characterizes the biological and hydrodynamic components of two Southern California LIEs, Los Peñasquitos Lagoon (LPL) and San Diego Bay (SDB). In LPL, in situ oyster valvometry and environmental observations distinguished the behavior of near-surface and near-bottom Magallana gigas oysters on tidal, diurnal, and tidally averaged time scales. Near-surface oysters responded strongly to salinity and dissolved oxygen, opened and closed in phase with solar insolation, and closed consistently during low tides, whereas near-bottom oysters responded weakly to measured variables, with a lagged response to insolation and a weak response to tidal phase. In SDB, a high-resolution hydrodynamic model of the tidally averaged exchange flow verified previously observed salinity and temperature regimes and revealed their seasonally varying circulation. During summer, SDB exhibited classical thermally driven circulation near the mouth, with warm outflows over colder bottom inflows, and inverse circulation near the head, with salty bottom outflows. Fall cooling drove entire-bay inverse circulation, broken by late winter and spring river flows driving entire-bay classical circulation. These circulation cells are sensitive to atmospheric forcing; the dry year 2018 showed only brief classical circulation compared with wetter years. Lagrangian particle tracking then resolved spatial and interannual variability in SDB residence times, which was compared with a decade of oyster recruitment observations and environmental records. Recruitment increased toward the estuary head, consistent with headward increases in temperature, salinity, and residence time. Residence times were longest near the head in 2018, approximately double those of 2017 and 2019. Recruitment was significantly related to median air temperature, wind speed, sea surface temperature, and coastal upwelling. This work advances understanding of biophysical interactions and hydrodynamic processes in LIEs, with relevance to estuary management in San Diego and to coastal communities generally.