Includes bibliographical references. / An observational study was undertaken to determine the seasonality of the marine carbonate system of the southern Benguela focusing on three key points: the processes driving bulk stoichiometry, alkalinity production on the continental shelf, and the air-sea flux of CO2. Monthly samples were taken along the St. Helena Bay Monitoring Line in the southern Benguela for ten of the months in 2010. Samples were analysed for dissolved inorganic carbon (DIC) and total alkalinity (TA). Temperature, salinity, oxygen and nutrients were also measured.

All wave-theoretic underwater sound propagation models attempt to derive the acoustic field originating from a sound source in a specific environment by either solving the wave equation directly or by solving an approximation there-of. This dissertation describes a normal mode direct solution with emphasis on the application as well as the theoretic analysis capability of the specific model, called NORMAN.

The Benguela Upwelling System (BUS) on the west coast of southern Africa is one of the global ocean’s most productive upwelling systems supporting a large fishing industry, a fledgling aquaculture sector and offshore mining interests. Despite intensive monitoring and modelling studies, there is no regionally tailored ocean forecasting system that is explicitly developed to deal with the unique ocean dynamics of the Benguela. In this study, the Hybrid Coordinate Ocean Model (HYCOM) is used in conjunction with the Ensemble Optimal Interpolation (EnOI) assimilation scheme to study the impact of assimilating sea surface temperature (SST) and along-track sea level anomalies (SLA) observations on predicted upwelling dynamics in the Benguela. In order to evaluate the predictive skill and impact of data assimilation, three experiments with HYCOMEnOI are evaluated: (1) with no assimilation (HYCOMFREE), (2) only assimilating along-track SLA (HYCOMSLA) and (3) assimilating both SLA and SST (HYCOMSLA+SST). Using MODIS Terra SST as reference, the model SST outputs are evaluated. HYCOMFREE is found to exhibit a warm bias along the coast, HYCOMSLA shows an even greater warm bias while HYCOMSLA+SST conversely shows a much improved SST forecast skill. It is hypothesised that the warm biases could be due to errors in boundary conditions and/or the ERA-interim wind product used to force the model. Furthermore, a comparison of the assimilated SST product (the Operational Sea Surface Temperature and Sea Ice Analysis; OSTIA) with MODIS SST reveals biases in OSTIA up to ±1 ◦C, raising questions over its suitability for assimilation in upwelling regions. Studying the effect of assimilation on SSH, SST and surface currents before and after the assimilation suggests that an increase in SSH from assimilated SLA leads to increased warm SST biases in HYCOMSLA. This is due to an incorrect relationship between SSH and SST in the free-running HYCOM, from which the static ensemble is derived for the EnOI. HYCOMSLA+SST exhibits slightly enhanced SSH increments but the associated increase in SST is significantly reduced by the assimilated SST, resulting in a reduction of the bias with very little impact on the current dynamics. This is reflected in the surface velocitiy increments, which are similar to or worse than that of HYCOMSLA. Investigating the potential of HYCOM-EnOI as an operational forecasting system has revealed that the assimilation of SST and along-track SLA vastly improves modelled SST for the BUS upwelling. Errors in the free-running model, which constitutes the static ensemble, need addressing and comparisons between MODIS and OSTIA SSTs suggests that OSTIA may not be ideally suited for assimilation in the case of coastal upwelling, due to limitations in capturing the dynamics correctly.

The land-sea breeze is resonant with the inertial response of the ocean at the critical latitude of 30° N/S, however its role in the physical and biogeochemical functioning of eastern boundary upwelling systems (EBUS) is often over-looked. Here, we present a series of 1D, 2D, and 3D numerical experiments which elucidate the drivers of diurnal-inertial variability and vertical mixing in EBUS due to land-sea breeze forcing near the critical latitude. The amplitude of the diurnal anticyclonic rotary component of the wind stress (τ ac0 ) is shown to be a good predictor of the locally forced response. The water depth plays an important role, where for shallow water depths (<∼100 m) surface oscillations are dampened and shear-driven mixing at the thermocline is reduced. Convergence/ divergence of the forced surface oscillations drive evanescent internal waves which elevate local vertical mixing above that from the forced response alone. The internal wave response is dampened by a gradually sloping bottom topography. St Helena Bay (∼32.5° S), in the southern Benguela upwelling system, possesses a combination of physical characteristics which favour an enhanced response to the land-sea breeze, namely a near-critical latitude, a local enhancement of τ ac0 , and a tendency for the development of a shallow stratified surface layer. Here, land-sea breeze forcing contributes to large diurnal variability in sea surface temperatures (SST's). During relaxation events, mean SST's are notably reduced due to land-sea breeze-driven vertical mixing. During upwelling events, the land-sea breeze drives a net warming of inner shelf waters primarily due to enhanced retention of the deepened surface mixed layer. The deepened thermocline impacts geostrophically-driven alongshore currents within St Helena Bay, which are strengthened (weakened) during upwelling (relaxation) events. It appears likely that the land-sea breeze plays an important role in the productivity of the system.

Madagascar’s southern coastal marine zone is a region of high biological productivity which supports a wide range of marine ecosystems, including fisheries. This high biological productivity is attributed to coastal upwelling. The thesis seeks to characterise the variability of the coastal upwelling south of Madagascar. The first part of the thesis provides new insights on the structure, variability and drivers of the coastal upwelling south of Madagascar. Satellite remote sensing is used to characterize the spatial extent and strength of the coastal upwelling. A front detection algorithm is applied to thirteen years of Multi-scale Ultra-high Resolution (MUR) Sea Surface Temperatures (SST) and an upwelling index is calculated. The influence of winds and ocean currents as drivers of the upwelling are investigated using satellite, in-situ observations, and a numerical model. Results reveal the presence of two well-defined upwelling cells. The first cell (Core 1) is located in the southeastern corner of Madagascar, and the second cell (Core 2) is west of the southern tip of Madagascar. These two cores are characterized by different seasonal variability, different intensities, different upwelled water mass origins, and distinct forcing mechanisms. Core 1 is associated with a dynamical upwelling forced by the detachment of the East Madagascar Current (EMC), which is reinforced by upwelling favourable winds. Core 2 which appears to be primarily forced by upwelling favourable winds, is also influenced by a poleward eastern boundary flow coming from the Mozambique Channel. This intrusion of Mozambique Channel warm waters could result in an asynchronicity in seasonality between upwelling surface signature and upwelling favourables winds. The second part of the thesis focuses on the interaction between the intrusion of warm water from Mozambique channel and the upwelling cell in Core 2. Cruise datasets, satellite remote sensing observations and model data analyses are combined to highlight the existence of a coastal surface poleward flow in the south-west of Madagascar: the South-west MAdagascar iv Coastal Current (SMACC). The SMACC is a relatively shallow (Coastal Current (SMACC). The SMACC is a relatively shallow (<300 m) and narrow (<100km wide) warm and salty coastal surface current, which flows along the south western coast of Madagascar toward the south, opposite to the dominant winds. The warm water surface signature of the SMACC extends from 22◦S (upstream) to 26.4◦S (downstream). The SMACC exhibits a seasonal variability: more intense in summer and reduced in winter. The average volume transport of its core is about 1.3 Sv with a mean summer maximum of 2.1 Sv. It is forced by a strong cyclonic wind stress curl associated with the bending of the trade winds along the southern tip of Madagascar. The SMACC directly influences the coastal upwelling regions south of Madagascar. Its existence is likely to influence local fisheries and larval transportpatterns, as well as the connectivity with the Agulhas Current, affecting the returning branch of the global overturning circulation. The last part of the thesis provides a holistic understanding of the inter-annual variability of the upwelling cells associated with the multiple forcing mechanisms defined in the first two parts of this work. Results reveal that the upwelling cells, Core 1 and Core 2, have different inter-annual variabilities. Inter-annual variability of Core 1 is associated with the East Madagascar Current (EMC) while Core 2 is linked with the South-west MAdagascar Coastal Current (SMACC). Inter-annual changes in the EMC occur as a result of oscillations in the South Equatorial Current (SEC) bifurcation off Madagascar, while the inter-annual variability in the SMACC is influenced by the cyclonic wind stress curl inter-annual variability. The upwelling is also linked with global/regional climate modes. Both Cores are highly correlated with the Subtropical Indian Ocean Dipole (SIOD). Core 2 is also correlated to the Indian Ocean Dipole (IOD). Both cores are significantly correlated with the El Ni˜no-Southern Oscillation (ENSO) after 12 months lag.

The thesis aims to seek to document the long-term change and decadal variability in the Benguela Upwelling System and study the possible mechanisms behind these changes. The Benguela Upwelling System is one of the four most productive fisheries areas in the world, and it is therefore important to understand the mechanisms leading to changes at different time and space scales before developing scenarios or forecasts for the future of the region. The first part of the thesis (chapter 3) uses four satellite-derived Sea Surface Temperature (SST) datasets combined with various climate reanalysis data to investigate the long-term SST trends in the Benguela Upwelling System over the period 1982-2017. The use of different datasets shows different trends depending on the dataset, which is a concern. However, after a thorough examination, there is some consensus. Results show that the Angola-Benguela Upwelling System has significantly changed during the last three decades. The changes vary in space and depend on season. Cooling trends are observed in the southern part of the Benguela Upwelling System in the austral summer and autumn. The cooling trend is consistent with a positive trend in upwelling-favourable equatorward winds due to the intensification and poleward expansion of the South Atlantic Subtropical high-pressure atmospheric system. A warming trend is observed in Southern Angola and Northern Benguela in late spring and summer. Results also show that the warming or cooling trends in the Benguela Upwelling System are not as linear as the trend in global air temperature. Indeed, when studying trends for the 1982-2017 period, trends tend to slow down and can reverse sign in some regions and recent time, suggesting decadal variability. Most discrepancy between SST datasets occurs from 1982 to 1985, the start of the satellite era. The second part of the thesis (chapter 4) focuses on understanding the mechanisms leading to the warming trends along the Angolan and Northern Benguela coast. To do so, the Ocean General Circulation Model NEMO (OGCM NEMO) is used. The model produces an unrealistic cooling trend in the Northern Benguela due to a positive trend in upwelling-favourable wind model forcing. The modelled warming trend in Southern Angola is properly simulated which allows me to use the model to study the mechanisms leading to the warming trend in Angola. Analysis of the model net heat budget components and their contribution to the overall SST trend suggests that the warming trend observed along the Angolan and Namibian coasts through the austral summer is primarily associated with the intensification of the poleward flow along the coast, bringing more warm water from the tropics to the region and also due to weakening of the vertical flow of cold water to the surface. Locally, the net surface heat flux has decreased and tends to create a negative SST trend but does not offset the warming trend created by the intensification of the flow. The poleward intensification of the Angola Current is attributed to the intensification of the cyclonic circulation around the Angola Dome. Lastly, in chapter 5, the decadal variability in the Benguela upwelling system, identified in Chapter 3, is investigated using a long-term ocean model simulation of 110 years (1900 - 2010) of the global ocean-ice components of the Norwegian Earth System Model (NorESM). The results reveal the presence of three dominant scales of variability: the interannual (2-8 years), quasi-decadal (9-14 years) and interdecadal (19-26 years) variability in the Southern Benguela upwelling system. The Southern Benguela SST correlations with the global SST reveal that at quasi-decadal scale the Southern Benguela SST is linked to the south Atlantic SST and the north-east Pacific SST fluctuations, while at the interdecadal scale the Southern Benguela SST modulation is linked to the equatorial and northern Pacific SST, Indian SST and Atlantic SST fluctuations except the equatorial Atlantic SST.

Geophysical fluid dynamics (GFD) models have progressed greatly in simulating the world’s oceans and estuaries in the past three decades, thanks to the development of novel numerical algorithms and the advent of massively parallel high-performance computing platforms. Study of inter-related processes on multi-scales (e.g., between large-scale (remote) processes and small-scale (local) processes) has always been an important theme for GFD modeling. For this purpose, models based on unstructured-grid (UG) have shown great potential because of their superior abilities in enabling multi-resolution and in fitting geometry and boundary. Despite UG models’ successful applications on coastal systems, significant obstacles still exist that have so far prevented UG models from realizing their full cross-scale capability. The pressing issues include the computation overhead resulting from large contrasts in the spatial resolutions, and the relative lack of skill for UG model in the eddying regime. Specifically for our own implicit UG model (SCHISM), the transport solver often emerges as a major bottleneck for both accuracy and efficiency. The overall goal of this dissertation is two-fold. The first goal is to address the challenges in tracer transport by developing efficient high-order schemes for the transport processes and test them in the framework of a community supported modeling system (SCHISM: Semi-implicit Cross-scale Hydroscience Integrated System Model) for cross-scale processes. The second goal is to utilize the new schemes developed in this dissertation and elsewhere to build a bona fide cross-scale Chesapeake Bay model and use it to address some key knowledge gaps in the physical processes in this system and to better assist decision makers of coastal resource management. The work on numerical scheme development has resulted in two new high-order transport solvers. The first solver tackles the vertical transport that often imposes the most stringent constraint on model efficiency (Chapter 2). With an implicit method and two flux limiters in both space and time, the new TVD2 solver leads to a speed-up of 1.6-6.0 in various cross-scale applications as compared to traditional explicit methods, while achieving 2nd-order accuracy in both space and time. Together with a flexible vertical gridding system, the flow over steep slopes can be faithfully simulated efficiently and accurately without altering the underlying bathymetry. The second scheme aims at improving the model skill in the eddying ocean (Chapter 4). UG coastal models tend to under-resolve features like meso-scale eddies and meanders, and this issue is partially attributed to the numerical diffusion in the transport schemes that are originally developed for estuarine applications. to address this issue, a 3rd-order transport scheme based on WENO formulation is developed, and is demonstrated to improve the meso-scale features. The new solvers are then tested in the Chesapeake Bay and adjacent Atlantic Ocean on small, medium and large domains respectively, corresponding to the three main chapters of this dissertation (Chapter 2-4), with an ultimate goal of achieving a seamless cross-scale model from the Gulf Stream to the shallow regions in the Bay tributaries and sub-tributaries. We highlight the dominant role played by the bathymetry in nearshore systems and the detrimental effects of bathymetric smoothing commonly used in many coastal models (Chapter 3). With the new methods developed in this dissertation and elsewhere, the model has enabled the analyses on some important processes that are hard to quantify with traditional techniques, e.g., the effect of channel-shoal contrast on lateral circulation and salinity distribution, hypoxia volume, the influence of realistic bathymetry on the freshwater plume etc. Potential topics for future research are also discussed at the end. In addition, the new solvers have also been successfully exported to many other oceanic and nearshore systems around the world via user groups of our community modeling system (cf. ‘Publications’ under ‘schism.wiki’).

Nitrogen is an essential component for life. The natural nitrogen cycle has been greatly disturbed by the production of fertilizer and use of fossil fuels, such that it has doubled the amount of reactive nitrogen (Nr) produced globally. Excessive additions of Nr to the environment can have negative effects, including eutrophication, loss of biodiversity, enhanced greenhouse gas emissions, acidification, increased tropospheric ozone, and damage to human health. Excess ammonia (NH3) and nitrogen oxide (NOx) emissions lead to increased aerosol loading via secondary aerosol formation processes. Increased aerosol loading has impacts on the climate and on human health. Furthermore, the aerosols formed from Nr from continental sources can get deposited to the open ocean, which is usually nitrogen limited. Knowing the concentrations of different aerosol species from a pollution free environment, such as the remote open ocean, can give insights into the natural preindustrial conditions and be used as a baseline for looking into the impacts of anthropogenic activities. This thesis focuses on establishing the Cape Point Global Atmosphere Watch (GAW) station as a site for collecting aerosol samples from pristine marine air masses. The use of a tower site allows for high temporal resolution sampling across multiple seasons and years, which is logistically difficult when relying on ship-based sampling of pristine marine environments. Results are presented from the chemical composition analysis of aerosols sampled at the Cape Point GAW station, including comparisons of two different aerosol sampling systems (tall-tower PM10 and ground-based sizesegregated). Furthermore, the installation and testing of a sector-controlled sampling system designed to reduce continental influence on samples is evaluated. Air mass back trajectories and radon (222Rn) concentrations were used to classify the air masses of each aerosol sample as either marine, modified marine, or continental. We found that continental samples had elevated concentrations of NH4 + , NO3 - , and non-sea-salt SO4 2- , whereas the marine samples had elevated concentrations of Cl- , and Na+ , as expected. A comparison of the tall-tower PM10 and ground-based size-segregated sampling systems showed that the ground-based sampler measured higher concentrations of coarse mode aerosols. This is attributed to the settling of large aerosols within the long sampling intake tube from the tower sampling system. The sector-controlled sampling system based on wind speed and direction was able to remove some of the influence of continental air masses, however some continental influence could not be avoided as the continental air masses circulated over the ocean before being sampled from the marine sector. This system could be improved by having additional cut-off limits defined for sampling, such as particle number, black carbon, or carbon monoxide (CO) concentrations.

The Prince Edward Islands (PEIs) Archipelago are situated in a prime location for the study of ecosystem response to intrinsic climate variability in the Southern Ocean and the impact of climate change. They are positioned in the Polar Frontal Zone, which is constrained by the subAntarctic Front and the Antarctic Polar Front, all of which are part of the strong, uninterrupted Antarctic Circumpolar Current (ACC). Due to its remoteness and challenging accessibility, there is a severe lack of data in the Southern Ocean and at the PEIs. The existing data are only available as single points observations or snapshots from past research cruises. This study thus makes use of 23 years (1993 – 2016) of satellite and reanalysis data to determine the annual/interannual and long-term variability of Sea Surface Temperature (SST), wind forcing and surface circulation at the PEIs and determine whether natural modes of climate variability like the El Niño Southern Oscillation (ENSO), Southern Annular Mode (SAM) or SemiAnnual Oscillation (SAO) were affecting these parameters. SST, wind speed, wind stress curl and the Ekman current did not express any long-term trend. A significant increasing but very small trend was only perceived in the geostrophic current and total surface current which was concluded to not be associated with the intensification of the ACC caused by a more positive SAM phase. The anomalies in SST showed striking interannual variability at a periodicity of 0.8, 2.8 and 7.5 years showing a similar pattern to that of ENSO with a periodicity of 1.5, 2.9 and 6 years. There has however been no relationship established between SST and any of the climate modes, but the Antarctic Circumpolar Wave (ACW), which is one of ENSO's teleconnection, could be responsible for the interannual changes seen in the SST anomalies. The anomalies in wind speed did not show any apparent periodicity and no relationship with ENSO. More so, while the impact of SAM and SAO has been seen on the westerly wind belt which governs the latitude of the PEIs, no correlation was established between the wind speed at the islands and SAM or SAO. The anomalies in wind stress curl presented no visible interannual variability but some sign of short-term variability. There was also no link 2 established between wind stress curl at the PEIs and any of the climate modes. Finally, a periodicity of 1.3 and 4 years was seen in the geostrophic current anomalies which also coincided with the pattern of ENSO but only showed minor correlation with ENSO. The ACW was deduced to perhaps also be responsible for the surface currents anomalies since the ACW is primarily propagated within the ACC. The trends perceived in the parameters considered for this study and the impact of climate modes on them appeared to be different to patterns which has been historically observed across the Southern Ocean. This further confirms the fact that the neighbouring oceanography and surface wind speed variability surrounding the PEIs differ from other regions of the Southern Ocean, most probably due to the frequent mesoscale instability such as eddies and frontal movement influencing the region. The impact of climate change on the PEIs ecosystem thus cannot be expected to be the same as the rest of the Southern Ocean.

Multiple natural and anthropogenic drivers are expanding the variability of the estuarine carbonate system (CO2 system). These changes in the CO2 system are threatening the health of ecologically and economically important bivalve species. This dissertation investigates the Chesapeake Bay CO2 system by using numerical models and historical water quality data, focusing on the past three decades, the contemporary period, and the late 2060s. In Chapter 2, sensitivity experiments are conducted with a 3-D Chesapeake Bay hydrodynamic-biogeochemical model and reveal that the magnitude of decadal trends in the CO2 system over the past 30 years is much greater than that observed in the open ocean. This is due to a combination of impacts from the land, atmosphere, and ocean. The greatest surface pH and aragonite saturation state (Ω_AR) reductions have occurred in the summer in the mesohaline Bay (–0.24 units and –0.9 over the past 30 years, respectively), with nearly equal influences from increased atmospheric CO2 and reduced nutrient loading. Increases in riverine total alkalinity (TA) and dissolved inorganic carbon (DIC) have raised surface pH in the upper oligohaline Bay. On top of these long-term trends, short-term CO2 system variability is particularly pronounced in smaller tributaries of the Chesapeake Bay. These relatively shallow regions are important sites for the shellfish aquaculture industry as well as oyster restoration, and could be more susceptible to coastal acidification due to terrestrial runoff. Chapter 3 examines the primary controls of the CO2 system in a tidal estuary of the Chesapeake Bay: the York River Estuary (YRE). Model results show that on average, wetland inputs account for 27% and 20% of the total DIC and TA inputs to the estuary, respectively. In addition, wetlands increase estuarine CO2 outgassing by a factor of two relative to a simulation without wetlands. Strong quasi-monthly variability in DIC and TA is driven by tidal cycles, which cause fluctuations between net heterotrophy and net autotrophy. Model results in a wetter year compared to those in a drier year show that greater net heterotrophy is largely responsible for a tripled net biological DIC production and the increased CO2 outgassing in the wetter year. Chapter 4 investigates the impact of extreme river discharge and climate change on calcium carbonate saturation state (Ω_Ca) in the YRE. Model results show that year-to-year differences in river discharge produce differences in Ω_Ca that are comparable in magnitude to the long-term reductions in Ω_Ca projected to occur over the next 50 years. Although a similar high discharge event in the future will have 20–40% less of an impact on Ω_Ca, increasing atmospheric CO2 will decrease baseline Ω_Ca. Shallow regions in the lower YRE, where most oyster reefs are located, typically recover faster after a high discharge event compared to regions farther upstream. This dissertation complements existing knowledge on Chesapeake Bay CO2 system and provides useful information to regional stakeholders. Local managers need to know the causes of acidification over different spatiotemporal scales, and specifically what portion is due to drivers they can control (e.g., nutrient reductions) versus drivers they have less control (e.g., climate change). These analyses of the CO2 system variability at spatiotemporal scales that are relevant to the Bay’s shellfish industry provide information regarding environmental challenges that the industry faces today and will likely face more often in the future.