UC Berkeley

San Francisco Bay sits within a highly urbanized community and is home to endangered species and fish nurseries. The surrounding dense population creates large wastewater effluent resulting in high nutrient levels in the estuary. Scientists wonder why there have not been annual phytoplankton blooms as observed in other estuaries with lower nutrient levels such as the Chesapeake Bay \cite{Boynton:1995}. 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.

This dissertation breaks down the mechanics responsible for observed development of stratification over the ebb tide and destratification at the end of ebb to mid flood tides. Results reveal longitudinal mechanics are primarily responsible for development and destruction of stratification at times of high velocity. During tide transitions, lateral exchange allows for the interaction of perimeter-shoal waters. Seasonal differences in salinity and water temperature are observed in order to develop an understanding of how the estuary responds to various climates. Seasonal trends indicate changes in precipitation lead to high variability of the magnitude and range of salinity, magnitude of stratification, and perimeter water temperature. Salinity and temperature observations are used to calculate residence time and longitudinal dispersion rates for Lower South San Francisco Bay. Present-day conditions reveal stratification is broken down on each tide, but further research should be done applying these observed salinity and temperature gradients with adjustments for potential future climate conditions.