This report is the final report of an investigation of water levels, current profiles, and water temperatures in order to determine dominant factors controlling San Diego Bay circulation, flusing, and movement of pollutants, with the data used to validate water circulation models and to make them more predictive.

Nearshore waters are governed by complex hydrodynamic interactions within landscapes that vary globally. Many of these often-energetic flows are intricate, diverse, and fine-scale, making holistic understanding difficult. Advancements in computational processing, coupled with ever growing environmental datasets and refining remote sensing technologies, offer new opportunities to constrain the controls behind these processes. This dissertation investigates complex, important nearshore hydrodynamics through applications of remote sensing technologies and data analysis. Focusing on the nearshore ocean off the geomorphologically diverse coastline of Northern California, we develop and implement novel methodologies to observe, quantify, and analyze fine-scale processes in each chapter of this dissertation, thereby illuminating coastal hydrodynamics that have been difficult to monitor.

In chapter 1, we analyze the dispersion of turbid freshwater plumes from the Russian River, California, a prototypical small mountainous river system. River plumes of this size, although common and vital in Mediterranean climate regions, have been understudied, leading to significant gaps in understanding. Using 15 years of daily MODIS satellite imagery and environmental data, we reveal the interplay of river discharge, waves, winds, and tides in shaping plume behavior. This analysis serves as a ground truth for previous studies and uncovers previously undiscussed patterns of small to moderate sized river plume dynamics.

Chapter 2 presents a methodology that enhances nearshore temperature monitoring capabilities by utilizing calibration data between high-resolution (100m) Landsat thermal infrared data and coincident moderate resolution (1km) MODIS sea surface temperature (SST) data. Data calibrated by this methodology is tested against in-situ measurements at various distances from the Northern California coast and presents use cases for this high-resolution dataset, demonstrating significant advancement over traditional SST products and offering initial insights into fine-scale temperature mixing processes.

In Chapter 3, we investigate wave-driven cross-shore sediment transport using high resolution (10m) Sentinel-2 remote sensing data, enhanced by machine learning post-processing utilized to resolve nearshore heterogeneity. By isolating turbid water signals and analyzing them alongside wave model data, tidal data, and high resolution (2m) bathymetric data, we characterize sediment transport dynamics across diverse coastal facies. This work constrains how the interplay between wave climate, bathymetric complexity, and sediment availability influences the extent and patterns of offshore turbidity transport in both sandy and rocky environments.

Collectively, the studies in this dissertation advance our understanding of nearshore hydrodynamics by leveraging remote sensing and data analysis constrain to their controls. The methodologies and findings presented here contribute to improved coastal monitoring, management, and research, with potential applications in similar coastal regions globally.

Eastern Boundary Upwelling Systems (EBUS) are highly productive biomes, which provide benefit to society and support local ecosystems. Although EBUS total area is small when compared to other pelagic ecosystems, a growing body of literature demonstrate that climate impacts on EBUS will have disproportionately large consequences for human society. Like other EBUS, the California Current System (CCS) is experiencing a number of inextricably linked stressors: acidification, oxygen stress (hypoxia), altered food webs, and warming temperatures. Each stressor has the potential to change species interactions; alter the abundance and distribution of organisms; and can even result in mortality for certain organisms. Wind forcing and freshwater input drive change in the coastal zone, and result in heterogeneous expression of multiple stressors in time and space. River-flow and winds are both anticipated to change in magnitude and timing due to human- and climate-induced changes, which drive associated impacts to physical and biogeochemical processes in estuaries and continental shelves. A step towards better understanding drivers of multiple stressor interactions includes analysis of subsurface observations to identify relationships and trends in shelf waters. In this work we focus on the physical dynamics which influence dissolved oxygen (DO) over the shelf off northern California and Washington, to better understand the physical dynamics that influence hypoxia. In the CCS, and other EBUS, high productivity is supported by coastal wind-driven upwelling that supplies the shelf with nutrient-rich waters. However, high rates of productivity in the coastal zone may operate at the expense of (1) decreasing aragonite and calcite saturation states and decreasing dissolved oxygen (DO) concentrations because the water that is upwelled to the continental shelf also has reduced DO levels, lower pH, and higher concentrations of dissolved inorganic carbon (DIC); and (2) high productivity maintains a high standing stock of particulate organic carbon (POC), which builds a respiration signal in the water column and at the sediment/water interface and results in a decline in DO. These are two mechanisms that make EBUS, including the CCS, prone to hypoxia and acidification, which threaten ecosystems and the communities they support. The coastal waters of Washington (and southern British Columbia) have the highest primary productivity in the CCS, but this high productivity is not co-located with the strongest upwelling-favorable alongshore winds (which occur off northern California). This mismatch has been explored (e.g, by Hickey and Banas 2008), and results point to additional mechanisms that facilitate the region's high productivity beyond the traditional focus of the coastal wind field. The work presented in this dissertation, to explore the physical dynamics which influence DO over the shelf in two regions of the CCS, was motivated by (1) the link between productivity and hypoxia (and the mismatch of productivity/wind forcing); (2) reports of extreme low DO observed off Washington in the summers of 2017 - 2019; and (3) a lack of subsurface DO time-series observations off northern California (where peak upwelling wind stress occurs). Two chapters of this dissertation focus on the central CCS (off northern California), a region for which which DO time-series are scarce; and one chapter addresses the northern CCS (off Washington) and is comprised of an analysis of a 10-year record of DO, temperature and salinity at multiple sites along with wind and river discharge data to better understand the timing and severity of shelf hypoxia.

Although the CCS is one of the most highly observed ocean regions in the world, there has been comparatively limited research on subsurface DO and carbonate system parameters in the central CCS off northern California (from 37°N to 42°N). Since long time-series of subsurface DO are relatively scarce, management decisions are made without a proper understanding of regional risk. Scientifically we are left wondering: (1) what DO levels occur in a section of the CCS that experiences the strongest upwelling favorable winds (~8x stronger than the Pacific Northwest)?; and (2) how DO levels respond to upwelling and relaxation events in this subregion? We collected time-series mooring data (temperature, salinity and DO), which are used to describe patterns and timing of hypoxia, and explore how DO levels respond to upwelling and relaxation events in the northern California coastal upwelling region. A deeper, mid-shelf site (~54m) is located in the Gulf of the Farallones, offshore San Francisco Bay, and within the more stratified upwelling shadow south of Point Reyes. The lowest DO concentrations and most persistent hypoxia were present at the mid-shelf site. At the shallower sites, (~18 and 30m), results show highly variable DO values with brief hypoxic events outside the core upwelling season (i.e., strongest winds and coldest water did not associate with the lowest DO levels). At the deeper, mid-shelf site, two distinct modes of variability were observed. During the first mode, upwelling events related to DO decline and relaxation events to increasing DO. During the second mode, the opposite occurs: upwelling related to an increase in DO and relaxation events to declining DO. At the shallower inner-shelf sites, and for the entire time-series, upwelling generally relates to DO decline and relaxation events to increasing DO. The importance of source water is clear during the first half of the mid-shelf deployment, and the overall trend and second half shows the importance of local drawdown. We also explored the seasonality of DO over a submarine bank (Cordell Bank) located at the shelf-break off northern California. Results show a recurrent seasonal cycle in temperature and DO. The similarity of seasonal patterns of temperature across years (2014 - 2018) is interesting, especially given the diverse set of oceanographic conditions the CCS experienced from 2014 – 2019. Although the coolest water occurs over the bank early in the upwelling season, the DO minimum occurs later, towards the end of the upwelling season and often during the relaxation season. Deviations from the seasonal trend observed are likely attributed to a combination of physical and biogeochemical processes working together. Specifically, we hypothesize that the interplay of wind-driven mixing and surface productivity can explain internanual differences, but additional work is needed to fully understand the role of these drivers. At Cordell Bank, DO concentrations were often below the threshold of mild hypoxia (2.45 ml/L), but only one instance of intermediate hypoxia was observed (1.4 to 2.45 ml/L) during the relaxation season (July 2017). Overall DO off northern California appears higher (fewer hypoxic events) than those observed in the northern CCS, but the upwelling favorable winds are also eight times stronger off northern California. Finally, observed DO is also lower than predicted using two source waters (PEW and PSUW) thus pointing to the likely importance of local drawdown (and potentially presence of more than two source water masses).

We focused on the physical dynamics which influence shelf DO in the northern CCS (off Washington), in attempt to better understand the physical dynamics that influenced the extreme low DO observed in the summers of 2017 - 2019. Mooring data (2011 - 2020) are used to describe the timing and severity of hypoxia off Washington. River and winds data (1991 - 2020) are also used to better understand the coastal environment and drivers of low DO. From this work we found significant interannual variability in DO. The 2016-2019 low DO period is statistically associated with spicier water, suggesting a link between source waters impacted by the El Niño, very, very low North Pacific Gyre Oscillation Index, marine heat wave presence and low DO over the shelf. When compared to historical DO records, summertime hypoxic exposure appears to have worsened on the Washington shelf. However, 2011 – 2020 shows significant interannual variability without a clear downward trend. We also observed a north-south trend with lower DO in the south, which can be explained by several hypotheses, ranging from shelf width to canyons to stratification. However, the relationship between stratification, surface salinity and DO is complex. Within periods with similar surface salinity, more stratification is related to lower DO, but overall higher stratification is caused by lower surface salinity and is associated with higher DO. This likely demonstrates a complex relationship between the presence of river water advected northward by downwelling-favorable winds and vertical mixing driven by downwelling. Additional work to further assess the impact of timing of the Columbia and Fraser Rivers relative to wind events is important to understand DO and carbonate chemistry off Washington, and help make predictions for future climate conditions.

Many coastal marine invertebrates and fish begin life as planktonic larvae that can be transported several kilometers offshore by coastal currents. To have any hope of surviving to reproduction, larvae must avoid predators during dispersal and return to shore with enough energy for further development. Most larvae fail to do so, prompting Rumrill (1990) to begin his review of larval mortality by stating that coastal marine animal larvae "lead transitory lives of great risk and grave uncertainty." I examine, using stochastic modeling, how these risks and uncertainties are shaped -- and in some cases, overcome -- by the passive and active interactions of larvae with spatially varying features of their environments. Chapter 2 focuses on the consequences of increased larval mortality near the coast compared with offshore. The relative safety of offshore waters is often mentioned in discussions of the evolutionary origins of planktonic larvae, but is omitted by most modeling studies. I show that ignoring this feature may, in some cases, substantially alter predictions of coastal population dynamics and connectivity. Furthermore, oceanographic features that slow nearshore larval movement (such as coastal boundary layers) are double-edged swords, limiting the offshore loss of larvae but also preventing larvae from escaping nearshore hazards.

Chapters 3 and 4 illustrate how larvae improve their chances of success by slowly swimming vertically to exploit differences in current velocity, food abundance, and predation throughout the water column. In Chapter 3, I consider a broad, continuous set of behaviors for larvae dispersing in an idealized environment approximating the two-layer flow typical of upwelling circulation. I show that while some behaviors successfully increase feeding opportunities and alongshore movement or limit the fraction of larvae that are lost offshore, no behaviors I modeled achieve both at once. I speculate that the former class of behaviors is suitable for organisms that spawn many cheap, long-lived larvae that feed during dispersal, while the latter is preferable for organisms with fewer, more expensive larvae that cannot feed. I extend this analysis in Chapter 4 by using dynamic programming to construct behaviors that optimize a metric of success that balances delivery to coastal habitats, predation risk, and energy budgeting. I demonstrate that some behaviors observed in nature are optimal in specific conditions, and that there exist realistic non-optimal behaviors that perform reliably well as conditions are varied. I hypothesize that many behaviors observed in nature result from selection for success in both typical or static conditions as well as extreme or variable ones. More broadly, I emphasize in Chapters 3 and 4 that predictable spatial structure in the environment creates an opportunity for larvae to change their destinies, and that these changes are most evident when mortality and energetics are considered alongside larval delivery to coastal habitats.

We will test the primary hypothesis that coastward advection of bottom cold-salty water during intense wind-driven upwelling provides conditions conducive forE. pacifica(the more oceanic species) to move onto the continental shelf where they become abundant and available to predators “early” in the season each year. As a corollary, we will test the hypothesis that as upwelling relaxes “later” in the season each year,E. pacificamoves offshore where it is less available to predators, andT. spinifera(the more coastal species) develops, becoming the dominant euphausiid in shelf waters and predator diets. 

Like most coastal states in the U.S., California’s shoreline communities and ecosystems have been exposed to flooding related to sea level rise and storms, which jeopardize their persistence and well-being. Shoreline transportation is especially vulnerable in certain places to flooding and failure, and because it is part of a continuously used network with little redundancy, it transfers its vulnerability to regional transportation networks. Forward-projected inundation/flooding risk is typically modeled at coarse spatial and temporal scales, which are useful at regional and decadal scales, but less useful for coastal managers and flood responders. This project improved assessment of both overall probability and short-term forecasts of water level for specific locations in San Francisco Bay that are vulnerable to flooding associated with sea level rise. The authors have developed probability assessment and forecasts through developing data-based, site-specific, model-independent approaches, which can be compared with and help to improve regional models of coastal flooding (e.g., CoSMoS). Water level data were collected across fine-scale arrays at fluvial-bay junctures in Sonoma and Marin Counties. The primary analysis is based on deconstructing water level records into multiple quasi-independent signals, which can be better predicted and recombined to produce probability of extreme events and to produce short-term forecasts during a flooding event based on predicted weather, wind, rain, and tide. In addition, real-time water level data are now available to first responders at critical locations in Novato Creek and Petaluma River when there is potential for flooding, as well as during a flood event. This is a pilot project that could be replicated at many other vulnerable locations around San Francisco Bay and elsewhere.

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