Coastal oceans are among the most dramatic, engaging, and dynamic locations the Earth has to offer. The Southern California Bight (SCB) is among those locations, full of iconic coastlines, economically important fisheries, marine protected areas, ports and shipping lanes, a national park, and a massive tourism industry. The SCB homes a diverse array of ecosystem types, ranging from rocky inner-tidal reef systems to giant kelp forests. The SCB also supports a coastal population of 23 million, making this a region of high human influence. Wastewater, rivers, and other sources of anthropogenic nutrients-enter this coastline in impressive quantities daily, heavily influencing the nutrient balance of coastal ecosystems. This dissertation provides a comprehensive analysis of anthropogenic nutrient influence in the context of micro and macro algae, first through a study of wastewater distribution, then through the impacts of kelp health through a nutrient stressed event. We also explore which regions would be most ideal to support kelp farming operations, amidst this anthropogenic influence.In Chapter 2, we present a mechanistic analysis of components of oceanic wastewater discharge in the SCB. Our goal was to understand productivity in the nearshore coastal area (0-15 km of coastline) and examine how it changes with and without chemical and physical components of the major wastewater plumes. We accomplish this by using five different scenarios of a wastewater model examining the mechanisms of buoyancy and inorganic nitrogen composition of outfall plumes. In this Chapter I demonstrate that the primary factors within treated wastewater that influence the productivity are the form of dissolved inorganic nitrogen and the buoyancy of the emitted plume. I show that the effects of increased buoyancy and nutrients on biomass are non-additive. Furthermore we identify a highly seasonal cycle in the influence of outfall scenarios on biomass in the surface ocean, with the largest impacts on NPP seen in the winter, when stratification in the water column is minimal. In Chapter 3, we illuminate the influence of anthropogenic nutrient inputs on the recovery and growth of giant kelp forests in the SCB. To do this we examine kelp forests before and amidst the 2014-2016 marine heat wave (MHW) an event which caused a large loss of kelp forest area. From this study we identify a significant positive relationship of anthropogenic nutrients and kelp forest area maintained through the 2014-2016 MHW. Additionally, we find that during this period there are large portions of the SCB that would be nutrient limited if not for anthropogenic inputs. In Chapter 4, we highlight the optimal locations in the SCB to cultivate giant kelp, and analyze the anthropogenic nutrient influence in these optimal locations. As demand for aquaculture, and in particular macroalgal cultivation, grows in the SCB, so has need for siting optimal locations. Our suitability analysis utilizes highly resolved biogeochemical models to find optimal nutrient (DIN), sunlight (PAR), and water temperature, as well as locational factors such as distance to port and depth in a rigorous spatial analysis framework, which builds upon others from this region. Our suitability results identifies highly suitable regions in the Santa Monica Bay and the Santa Barbara Channel. We find that of these two regions those located in Santa Monica Bay have the least potential interference with current kelp forest areas.

The abundance and size distribution of marine organic particles are two major factors controlling biological carbon sequestration in the ocean. These quantities are the result of complex physical-biological interactions that are difficult to observe, and their spatial and temporal patterns remain uncertain. This dissertation describes our analysis of particle size distributions (PSD) and the resulting export, from a global compilation of \textit{in situ} Underwater Vision Profiler 5 (UVP5) optical measurements.

In Chapter 2, we demostrate the ability to extrapolate sparse UVP5 observations to the global ocean from well-sampled oceanographic variables, using a machine learning algorithm. We reconstruct global maps of the biogenic PSD parameters (biovolume and slope) for particles at the base of the euphotic zone. These reconstructions reveal consistent global patterns, with high chlorophyll regions generally characterized by high particle biovolume and flatter PSD slope, i.e., a high relative abundance of large vs. small particles. The resulting negative correlations between particle biovolume and slope further suggest amplified effects on sinking particle fluxes. Our approach and estimates provide a baseline for understanding the export of organic matter from the surface ocean.

Chapter 3 describes how applying a simple empirical relationship to our reconstructions of the PSD, we can calculate the total export. In this Chapter, we explore the seasonal and spatial patterns of carbon export. Taking advantage of the high vertical resolution of the UVP5, we quantify the export from the surface using two previously established depth horizons. We identify a larger export from the Southern Ocean than most other models of export. Similarly, we find the lower part of the euphotic zone to be dominated by heterotrophy, rather than autotrophy. Being able to reconstruct the PSD and particle flux at multiple depths allows for further exploration of the full 3-dimensional particle field.

Chapter 4 describes a full 3-D model, where depth specific export is calculated, highlighting significant deviations from idealized flux profiles and quantify the efficiency of the biological pump globally. Our results reveal the primary drivers of carbon storage and sequestration and highlight the importance of transport by diel vertical migration of marine animals. These estimates of the global particle field serve as a baseline for future model-based estimates of particulate flux, and as an independent estimate of the efficiency of organic matter storage in the ocean.

In contrast to other biogeochemical tracers, nitrogen in the ocean exists in a myriad of chemical forms, each with its own distinct properties and reactivity. These diverse chemical forms of nitrogen, including organic and inorganic compounds, are collectively involved in a unique and dynamic microbially-mediated cycle which is tightly intertwined with the overall functioning of marine ecosystems and has significant implications for the global cycles of carbon, phosphorous, and oxygen. While nitrogen is predominantly cycled between bioavailable forms in the ocean, additional anaerobic metabolic pathways emerge when the concentration of dissolved oxygen drops to suboxic or anoxic levels within the ocean's oxygen-minimum-zones (OMZs). These pathways produce gaseous dinitrogen (N2) and nitrous oxide (N2O), a potent greenhouse agent and contributor to ozone depletion, which together lead to a loss of bioavailable nitrogen from the oceans to the atmosphere. This dissertation provides a comprehensive analysis of these microbial pathways in OMZs, and further explores their sensitivity to both physical and biogeochemical variability.

In Chapter 2, we describe the development of a general algorithm used to expand the observational record of a special class of subsurface, predominantly anticyclonic oceanic eddies known as submesoscale coherent vortices (SCVs). These eddies have been shown to play an oversized role in propagating water masses in the intermediate and deeper parts of the ocean, and were recently identified as hot-spots of N2 and N2O production. By applying the algorithm to the global Argo float array, we detect nearly 4000 new global observations of these eddies. Furthermore, we demonstrate that their formation takes place in regional hot-spots, allowing us to quantify their contributions to local heat and salt anomalies due to their formation and propagation.

In Chapter 3, we incorporate a new model of the oceanic nitrogen cycle into an eddy-resolving 3D regional ocean model of the Eastern Tropical South Pacific, an upwelling region and hot-spot of nitrogen loss and N2O outgassing. The model accurately simulates both aerobic and anaerobic transformations responsible for N2 and N2O production, and provides a realistic representation of the large scale physical circulation. By decomposing the N2O tracer in the 3D model, we are able to attribute contributions from local biogeochemical sources and sinks, explore the role of the physical circulation in supplying N2O to the region, and ultimately quantify the drivers of N2O outgassing to the atmosphere.

Finally, Chapter 4 builds upon the findings of Chapter 3. Specifically, we deploy a higher resolution version of the 3D model to explore how mesoscale-driven heterogeneity governs the production of N2 and N2O in the Eastern Tropical South Pacific. By filtering biogeochemical tracer fields into ``mean'' and ``eddy'' components (e.g., fields governed by low/high frequency and large/small spatial scales, respectively), we demonstrate that oxygen variability induced by ephemeral eddies and filaments stimulates nitrogen loss to the atmosphere, but by preferential producing N2 at the expense of N2O consumption. These findings reveal that the mesoscale circulation plays a critical role in regulating N2O production, and further implies that coarse-grained biogeochemical models may overestimate the fluxes to the atmosphere from these regions.

One of the major drivers of ecosystem changes is fishing, with global wild fish harvests increasing four times from the 1950s to 1990s. This spike depleted fish biomass and altered ecosystems. To assess these economic and ecological impacts, projects such as the Fisheries and Marine Ecosystem Model Intercomparison Project (FishMIP) have been undertaken. By designing numerical experiments, FishMIP aims to clarify long-term climate impacts on fisheries and marine ecosystems, reducing uncertainties- in model projections. One of the models in FishMIP is the BiOeconomic mArine Trophic Size-spectrum (BOATS)- that integrates ecology and economics to simulate global fishing history. For the last round of FishMIP simulations focused on model evaluation (ISIMIP3a), I compared BOATS simulations forced by climate reanalysis and forced with historical fishing effort reconstructions to real-world observations. The goal of comparison is to help disentangle the complex interplay between fishing, climate change, and ecosystem health, to strengthen confidence in projections and ultimately aiding in sustainable fisheries management and marine conservation. For this comparison I have worked with two versions of BOATS, the former v1, and a new v2 that includes an improved representation of biodiversity. By analyzing these two versions, I address the following questions: how well the BOATS model performs compared to the observation? What are the effects of climate variability and the effect of human drivers? To investigate climate variability, I generated Empirical Orthogonal Function (EOFs) for the driving variables of BOATS, temperature, NPP, particle flux, and for the modeled consumer biomass. For human drivers, I developed and implemented diagnostics at Large Marine Ecosystems (LMEs) level, including correlation coefficient, root mean square, maximum catch and biomass variation that quantify the biomass decline in each LMEs. The analysis shows that the two model versions provide similar results, both globally and across LMEs. I highlighted coherent patterns of match/mismatch with observations that shed light on remaining model biases in particular at regional scales, and suggest future research directions.

Eastern boundary upwelling systems (EBUSs) are among the most ecologically diverse and productive regions in the ocean. EBUSs account for approximately 1\% of the global ocean by area, but yields nearly 20\% of the global fish catch. Thus, consequences to changes in productivity in EBUSs anticipated under climate change span from regional socioeconomic stability to global food security. Ecological responses to wind-driven upwelling in EBUSs have long been studied, yet questions still remain on the controls of the cross-shore (zonal) ecosystem composition. Previous studies indicate that large plankton contribute to a majority of the biomass near the coast, where upwelling supports high levels of productivity, whereas small plankton account for most of the biomass in offshore regions with low productivity. However, little is known about the variations in zonal ecosystem composition with respect to perturbations in the large-scale physical forcing. In this thesis, I present a new quasi-2D, idealized physical model of EBUSs and a size structured ecosystem model, in which an organism’s size is chosen to represent ecological diversity. With this coupled physical-biogeochemical model, we characterize the zonal ecosystem composition and its responses to perturbations. These results are an important step toward understanding the sensitivities of plankton communities and higher food-web structure in EBUSs.