This project studies the fluxes of salt, temperature, suspended solids and phytoplankton between the San Francisco Bay and the coastal ocean. To do this, scientists measure current speeds along a transect across the mouth of the bay, a length of about 5 km. Salinity, temperature, turbidity and phytoplankton abundance will simultaneously be measured along the same transect.

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.

Over the past 3 years, we have pursued extensive research into the hydrodynamics of shallow water habitats in the Sacramento-San Joaquin Delta. The goal of these studies was to evaluate the relative importance of the various physical forcing mechanisms and influences, while developing the research tools required to address the dynamics of the systems. This work has led to larger-scale grants from CALFED and collaborations with the U.S. Geological Survey, which has facilitated extensive research into the hydrodynamics of shallow water habitats through a combination of field observations and numerical modeling.

Data from two sites has allowed us to begin the contrast the dynamics of different shallow water habitats in the Delta. The first site, Mildred Island, is influenced by forcing from the tides, wind and diurnal heating and cooling. The Island as a whole is a low energy environment, but the details of transport throughout the system are exceptionally subtle and complicated. To further evaluate the relative importance of each of these forcing mechanisms, an existing numerical model, TRIM-3d, has been applied to Mildred Island. After modification to allow for heating and cooling, the model has reproduced the primary trends in temperature over the timescales of several weeks. Using this model, we have evaluated residence times under various forcing conditions to conclude that wind and diurnal heating and cooling play an important role in determining the flushing of particular subregions within the Island.

The second site, Franks Tract, is dominated by tidal forcing and the interaction of tidal flows with vegetation, which develops on a seasonal timescale. Emphasis to this point has been on data analysis, and we have defined representative mean velocity profiles and surrogates for exchange between the vegetated and unvegetated regions of the flow. It appears that these exchanges are driven by intermittent flow instabilities which are likely to develop along the interface between vegetated and unvegetated regions of the flow.

Based on a combination of field observations and laboratory experiments, we have analyzed the annual and interannual salinity dynamics in a seasonal wetland in the San Joaquin Valley. The field observations, which included direct measurement of both the temporal and spatial variability in water velocities, conductivity, temperature an depth, suggest that the salinity dynamics in the wetland are dominated by advective transport processes which redistribute high salinity waters from the inlet throughout the wetland. As such, evapotranspiration and exchange between the soil column and the water column appear to play secondary roles in the salinity dynamics of the wetland. The conclusion regarding the role of soil column-water column exchange has been reinforced using laboratory experiments combined with numerical analysis, which indicate that the flux of salt between the soil and water columns is small in magnitude.

The work has been focused on observations of ocean-estuary exchange at the mouth of San Francisco Bay. The observational program consisted of 6 transect experiments, each capturing a complete 24-hour tidal day (with 2 exceptions due to instrument failures), spanning various seasons and tidal conditions. Using repeated transects of water velocity, conductivity, temperature, optical backscatter, and chlorophyll fluorescence, we have made great strides in developing a clear, quantitative understanding of ocean-estuary exchange in San Francisco Bay.

Shallow, bar-built estuaries on wave-dominated coasts in Mediterranean climates experience an intermittent connection to the ocean. Their inlets may completely close as a result of nearshore sand transport, but even the open condition these inlets remain constricted. Extensive field measurements in the highly salt-stratified Pescadero estuary in Northern California were made to elucidate hydrodynamic processes in these ecologically important yet understudied systems. Here we present unique detailed observations and a framework for understanding dynamics in small, shallow bar-built estuaries.

While closed, ocean water from waves overtopping the sand barrier and freshwater from two creeks maintain stratified conditions within the Pescadero estuary. Wind may cause hydraulic setup of the two-layer lagoon and induce mixing, but does not fully mix the water column. The transition from closed to open mouth states occurs when the sand barrier is breached and the lagoon drains and erodes this sand barrier. Fast drains are associated with full mixing of the water column, and a slow fall of the lagoon water level is associated with incomplete vertical mixing.

Observations show that in the open state, the shallow mouth causes these estuaries to experience discontinuous tidal forcing. While the ocean and estuary are fully connected with near equal water levels, tidal velocities are slow but infragravity motions in the nearshore cause large velocity oscillations. As the ocean tide falls, infragravity forcing is cut off because the estuarine mouth is perched above the low tide ocean water level, and ebbing velocities are set by bed friction. Observations reveal this oscillation between ocean-forced conditions and frictionally-controlled conditions characterizes and sets the hydrodynamics and salt dynamics in these estuaries. Additional wave setup of the lagoon water level emphasizes the dependence of these estuaries on nearshore ocean conditions, but the diurnal or semidiurnal retreat of the ocean below the mouth cuts off this nearshore influence. The salt field responds to this discontinuous forcing, being transported upstream on the flood and becoming trapped in deep pools of the estuary on ebb.

Longitudinal salt dispersion within the Pescadero estuary is calculated using velocity and salinity records. Dispersion of high salinity water was found to be an order of magnitude lower than dispersion of low salinity water. Vertical salinity measurements indicate that on the large ebb tide, high surface salinities rapidly relax, and a second pulse of salty water follows the relaxation. This pulse may induce vertical mixing in the fresher upper water column, and incites the high dispersion seen among low salinities. Upstream processes are implicated in trapping lower salinity water, while higher salinity water is bathymetrically restricted from marsh or shallow channel trapping.

Finally, observations were being made in the Pescadero estuary in March 2011 when the tsunami generated by the Tohoku earthquake arrived to the California coast. Measurements show that the presence of a tsunami-period signature in this shallow, bar-built estuary was modulated by tidal stage and that the tsunami-induced rise and fall of the ocean water level modulated the velocities seen within the estuary. The initial arrival of waves due to the tsunami caused some flushing of the estuary. Later, high velocities induced more mixing than typically seen in this estuary. After several days sand transport nearly choked closed the mouth of the estuary. These observations point to mechanisms which were likely important during the 2011 Tohoku tsunami in many Eastern Pacific estuaries.

This work addresses transport and mixing processes at work during each tide across the shoal-channel interface. These are fundamental to long-term, large-scale, salt, sediment and biomass budgets yet remain poorly characterized and understood. Most of the analyses presented here are based on field observations collected in South San Francisco Bay, CA, during winter 2009.

Horizontal transport across the interface is governed by the transverse flow, which is predominantly characterized by the presence of one or two lateral circulation cells. This study reveals that these circulation cells can evolve more rapidly than previously thought, reversing multiple times during a single ebb tide. The formation of convergence fronts is found to be sensitive to the direction of the lateral circulation and is therefore marked by a similar intratidal variability. It is hypothesized that these intratidal variations are the result of competing lateral density gradients which are the main forcing mechanism for transverse flows. The outcome of this competition depends strongly on vertical mixing conditions on the slope.

Vertical mixing on the slope is driven for the most part by turbulence generated in the bottom boundary layer, except for occasional late-ebb bursts generated by internal vertical shears. These internal shears result from the destabilizing straining of lateral shear by the lateral circulation which overcomes in this case the stabilizing straining of lateral density gradients.

Horizontal mixing across the interface is quantified indirectly and is found to be driven mostly by lateral shear instabilities, but is also affected by lateral dynamics. As a result, transverse mixing also displays significant intratidal variability. This result poses a challenge to existing parametrization developed for steady shear layers.

Sea-level rise (SLR) threatens coastal communities by increasing flood exposure for people, homes, businesses, and critical infrastructure. In order to protect residents and the infrastructure systems on which they rely, coastal communities will need to plan for and adapt to higher sea levels and increased flood hazards.

This dissertation contributes to the understanding of SLR impacts on human, engineered, and natural systems. More specifically, the text addresses three important aspects of SLR adaptation: the need for data-driven methods to inform regional SLR adaptation networks, the impacts of SLR on critical infrastructure and service disruptions, and the influence of coupled SLR, precipitation, and storm surge on coastal groundwater aquifers and flooding.

Many collaborative networks aimed at promoting SLR adaptation at the global, national, or regional scale are primarily based on geographic proximity or voluntary participation and are not grounded in any quantitative assessment of shared vulnerability. The first part of this dissertation presents a method to group communities based on similar SLR exposure variables using statistical cluster analysis. The method is applied to cities and counties in the San Francisco Bay Area to demonstrate the usefulness for developing regional SLR adaptation networks.

In coastal communities, critical infrastructure assets, such as wastewater treatment plants, are susceptible to flooding due to SLR. However, the extent and progression of this exposure and the impacts on service disruptions are poorly understood. The second part of this work presents a geospatial analysis of wastewater exposure to SLR-induced marine flooding at the national scale and a similar analysis of SLR-induced groundwater flooding at the regional scale in the San Francisco Bay Area. Overall, hundreds of wastewater treatment plants could face flood disruptions due to SLR, which could lead to a loss of wastewater services for millions of residents. In some cases, groundwater is more of a threat than marine flooding.

To understand the potential impacts of SLR on coastal groundwater aquifers and flooding, most previous studies have used steady-state methods and have focused on SLR and other climate factors, such as precipitation, separately. However, the strong coupling between precipitation and other weather variables that influence coastal water levels suggests a need for multivariate approaches. The final part of this dissertation describes the use of a copula approach to correlate precipitation with wind speed and atmospheric pressure. These variables are then used to determine changes in water levels due to wind setup and pressure-driven surge under current and future climate scenarios. Forcing a groundwater model with this data provides insight into the potential for a narrower unsaturated zone and groundwater emergence.

Together, these chapters explore the local disruptions and regional impacts of SLR, as well as the coupled processes that lead to flooding.

The antennules of many marine crustaceans enable them to rapidly locate sources of odorant in turbulent environmental flows. The antennules are typically flicked through the water, causing the animal to take spatially and temporally discrete odorant samples. A substantial gap in knowledge concerns how the physical interaction between chemosensory appendages and the chemical filaments forming a turbulent plume affects odorant detection and filters the information content of the plume. The research presented here is focused on using numerical models to simulate the flow of odorant-laden water around arrays of chemosensory aesthetascs, and the transport of odorant molecules to their surfaces, during a plume sampling event. The time-varying odorant flux signals generated during these events are of key interest, since they are the lens through which a plume tracking agent will perceive its odor environment.

Simulations of infinitely long arrays of sensory hairs indicate that there are likely to be design tradeoffs between maximizing the sharpness of an odorant flux signal versus the total amount of odorant mass detected. It is also clear that the duration of odorant flux during a sampling event similar to a flick downstroke is not long enough to enable detection of 0.6 mm wide odorant filaments by crustaceans such as lobsters, or by engineered chemical sensors currently available. This suggests that the return stroke and interflick pause may be critical if these animals are to detect fine-scale plume structures.

Models of hair arrays with a finite number of hairs reinforce the above conclusions, but because this more realistic geometry allows water to flow around the array of hairs in addition to through, it reveals additional behaviors that the infinite array simplification cannot capture. Fundamentally different trends in metrics describing the sharpness of the flux signal are observed for rapidly flicking, sparse arrays of hairs versus slowly moving, densely packed arrays. These surprising transitions are not well predicted by simple parameters describing only the fluid velocity field, pointing out the importance of explicitly modeling or observing odorant transport in addition to the flow of water.

A tomographic scan of a real aesthetasc array morphology, that of the spiny lobster P. argus, reveals substantial variation and deviation from any simple, idealized geometry, and 3D effects are likely to be important to its odorant sampling dynamics. Nonetheless, numerical simulations of an idealized version of P. argus morphology indicate that on average, odor-laden water is effectively channeled into the aesthetasc array as compared to a simple straight row of hairs. A simple row, however, still achieves greater odorant flux in most regards, again emphasizing differences in properties of the flow versus properties of passive scalar transport. Crustacean antennules might therefore best serve as starting iterations instead of optimal solutions for the design of engineered chemical sensor arrays for use on plume tracking robots.

California's Sacramento-San Joaquin Delta (the Delta) will experience tremendous change in the coming decades, as natural variation within the Delta confront wholesale background changes due to climate change, water shortages, potential levee failures, invasive species introduction, and anthropogenic management decisions. In light of this, I present work analyzing a number of facets of the Delta's physical functioning and how they might affect its ecological function.

Using a simple statistical water temperature model, we project water temperatures to warm across the region in the coming century, threatening species near ecological bottlenecks, and stressing other native populations. For example, timing of spring spawning temperatures for Delta smelt will shift earlier in the year. Lethal temperatures for Delta smelt will be more frequent in all four climate scenarios tested. I discuss possibilities for managing the Delta's thermal regime. I did field observations in Cache Slough in the north Delta to parse out smaller scale water temperature variations within a shallow tidal slough. Given bathymetric variation, velocity and thermal gradients develop, which mix and move throughout this complex region. These gradients can intensify near intersections, mixing out over tidal and diurnal cycles. Bathymetric variation combined with atmospheric heating/cooling create thermal gradients. Advection and diffusion move these gradients, which can be intensified where channel merge. Sharp gradients matter biologically; they also create possibilities for refugia for species pushed to their thermal limits. These gradients affect lateral flows, but lateral flows are more strongly affected by lateral wind forcing. Lateral circulation from wind is not strong enough to affect along-channel thermal mixing, as along-channel forcing is strong enough to overcome the homogenization driven by these lateral circulations.

In branching tidal systems, tidal dissipation, propagation and reflection together define the spatial distribution of tidal energy. When specific locations or regions are altered, for example through the restoration of tidal marsh, there is uncertainty as to how the system will respond, including the spatial influence of the changes. When tidal marsh habitat is restored, it creates local tidal dissipation which may alter tidal energy in other parts of the estuary, potentially altering the function of tidal marshes elsewhere. I present results of a simple analytic model of tidal propagation in a branching system. I developed wave equations for along-channel velocity and wave height which account for friction and changes in channel geometry. By linearizing the friction term in the depth-averaged along-channel momentum equation and including an amplification factor in the wave form, then combining it with the continuity equation, I solved for wave speed and amplification as a function of friction and channel geometry. I also solved for the tidal velocity and stage as a function of position and time. Using this solution within an idealized branching channel estuary and applying matching conditions at the branches, I analyzed the effects of changes to one branch on tidal regimes throughout an idealized branching channel estuary. I then applied this simple model to consider restoration questions on California's Sacramento-San Joaquin Delta.