<p> The circulation of the Southern Ocean is unique due to the lack of meridional boundaries at the latitudes of Drake Passage. Westerly winds drive the Antarctic Circumpolar Current (ACC), linking the major ocean basins and facilitating inter-basin exchange of properties. Additionally, the steeply tilted isopycnals in the Southern Ocean allow interaction between the deep ocean and the atmosphere, and as a result the Southern Ocean has an outsized contribution to the global uptake and redistribution of heat, carbon and nutrients. Complex topography and eddies make this circulation fundamentally three-dimensional, but many features and associated mechanisms of this three-dimensional circulation are not well understood. </p><p> The objective of this thesis is to use the 1/6&deg;, data-assimilating Southern Ocean State Estimate (SOSE), along with other high-resolution ocean models and available observations, to describe aspects of the three-dimensional structure of the upper cell of the Southern Ocean overturning circulation. First, we diagnose the upper ocean heat budget in the Southern Ocean (Chapter 2), and determine that a strong zonal asymmetry in the air-sea heat flux over the Southern Ocean is associated with large-scale meander the ACC mean path and associated asymmetry in geostrophic heat advection. Second, we use Lagrangian particle release experiments to show, for the first time, the full three-dimensional upwelling pathways of deep water from 30&deg;S to the surface of the Southern Ocean (Chapter 3). We find that deep water moves south in narrow paths along the western and eastern boundaries of each ocean basin, then within the ACC upwelling is concentrated at hotspots associated with high eddy activity at major topographic features. Next, we quantify the water mass transformation along the upwelling pathways from Chapter 3, and find that although the upwelling in the ocean interior is largely along isopycnals, there is significant transformation just below the mixed layer and homogenization of deep water mass properties due to isopycnal mixing (Chapter 4). Finally, we highlight a newly identified poleward pathway of deep water along the eastern boundary of the Indian Ocean and describe the structure and variability of this pathway (Chapter 5).</p><p>

Until 1982, when the National Research Institute for Oceanology (NRIO) erected self-contained, automatic weather stations (AWS) on the Cape South Coast, no continuous coastal measurements were available. This Institute had erected an AWS on the drilling rig Sedco K in 1978, so that over 3 years of very valuable off- shore data was already available on the adjacent Agulhas Bank. Al though the weather offices at George and Port Elizabeth have made accurate meteorological observations for over 30 years, this data is shown here to differ significantly from actual coastal measurements. Thus the NRIO AWS network, which operated for just over a year, provided a detailed, short-term data set for the study of coastal weather processes. In order to acquire longer term data from coastal observations, five years of hourly wind observations from lighthouse keepers along the Cape South Coast were also utilised. Although these are estimates, it is shown that a coastal estimate may be more representative of marine conditions than an anemometer reading some distance inland. Voluntary Observing Ship's data (VOS) extracted from SADCO's Marine Climatology database, provided the long-term offshore information, whilst also supplying very useful 'present weather' (synoptic code ww) observations for case studies. Observations from synoptic stations for the period that the coastal AWS were deployed (February 1982 - March 1983), were provided by the South African Weather Bureau. With this unique and comprehensive data set, the various weather systems affecting the region are discussed. Twelve case studies form the main reference for this discussion, which includes relevant oceanographic parameters. The weather systems are considered firstly as individually propagating circulations with the AWS network providing details of propagation speeds and coastwise development. Secondly the combined 'weather producing' effects of these systems are discussed, with a strong emphasis being placed on man/weather interactions. It is shown that certain operations along the Cape South Coast and over the Agulhas Bank, are extremely weather sensitive, and would benefit considerably from an increased knowledge of weather processes. Recommendations aimed not only at those managing weather sensitive operations, but also at those involved in coastal meteorological measurement and research, complete the thesis.

Includes bibliographical references. / The two principal bottom-up drivers of the High Nutrient Low Chlorophyll (HNLC) characteristics of the Southern Ocean are light and nutrient (mainly dissolved iron) limitation ( Boyd , 2002; Mitchell et al., 1991), which have varying limiting roles over the growing season ( Boyd, 2002; Swart et al., 2014). This research commenced with an investigation of the meridional characteristics of primary productivity in the Atlantic Southern Ocean during austral summer 2008.

The impact of El Niño Southern Oscillation (ENSO) on the Southern African inland climate is well documented and provides skill in the seasonal forecast of rainfall but little is known of the impact of ENSO on the ocean surrounding South Africa. The aim of this study is to assess the impact of ENSO on sea surface temperatures around the coast of South Africa and to calculate SST trends around the coast. I start by updating the study of Rouault et al (2010) on the very topic with an additional 10 years of data and two additional newer datasets which allow sampling closer to the coast where wind-driven upwelling is more active. The new highresolution ERA 5 reanalyzed climate dataset is also used to look at the atmospheric forcing of sea surface temperatures by ENSO. As in Rouault et al. (2010), I study five similar threedegree-long coastal regions around South Africa, namely: West Coast, South Coast, Port Elizabeth/Port Alfred, Transkei, Kwazulu-Natal and a larger offshore Agulhas Current area domain. Three SST datasets are evaluated in this study: the 1 ̊x1 ̊Optimal Interpolation sea surface temperature (OI SST) used by Rouault et al (2010), the 0.25 ̊x 0.25 ̊ Optimal Interpolation SST and the 4 km x 4 km Advanced Very High-Resolution Radiometer (AVHRR) Pathfinder SST version 5.3. The 0.25 ̊x 0.25 ̊OI SST resolvesSST anomalies better in these coastal regions as compared to 1 ̊x1 ̊ OISST. The difference in results among the three products concerning trends and correlation with ENSO is a cause for concern. The 4 km x 4 km AVHRR Pathfinder allows for SST to be extracted even closer to the coast but missing values are numerous and hamper the use of this dataset for ENSO composites and trend analyses. Results show a significant positive correlation with El Niño in summer at the monthly scale, reaching a maximum correlation of 0.45 at 3 months lag. Correlation is the highest in late summer. There is a negative correlation in the Agulhas Current area, opposite to those with ENSO and West Coast. The impact of ENSO on the coast of South Africa, West Coast and South Coast is due to change in surface wind speed with weaker upwelling favorable during El Niño leading to warmer than normal coastal water SST and stronger than normal Southeasterly winds during la Niña leading to cooler than normal coastal water. The wind perturbation is part of largescale basin-wide perturbations in the tropical Atlantic, in the South Atlantic high-pressure atmospheric system and in the westerly wind pattern of the midlatitude to the south. Non-ENSO related impact can be as important as ENSO related SST perturbation and is also linked to large scale perturbations in the South Atlantic. There is no relation between the strength of ENSO and the strength of the perturbation, and some ENSO events do not lead to the expected canonical warming or cooling. The large-scale SST perturbations seem to be caused by anomalous surface turbulent flux of latent and sensible heat and abnormal wind speed and direction. This study opens the possibility of seasonal forecasting of SST in the South Benguela upwelling system because of the positive lag correlation between ENSO and SST with ENSO leading SST.

Sea level rise and variability is of great concern in the coastal areas where a significant part of the global population is settled. Therefore, understanding regional and local long-term sea level variability as well as its trend is critical. On the other hand, quantifying how the sea level has varied on different timescales and why, is critical for understanding sea level changes, and crucial for improving future global, regional, and local projections. In this study, monthly mean sea level records of seven individual tide gauges, from the east and south coast of South Africa were used to analyse the embedded timescales of variability. These timescales were separated through the Empirical Mode Decomposition (EMD) method. This is the first time that the EMD method has been applied to southern African tide gauge records. The sensitivity of the EMD method when dealing with data gaps was tested on artificially created gaps in monthly mean synthetic altimetry sea level records, representing the seven individual tide gauges under consideration. The missing values were filled by linear interpolation, average value and linear trend value. The results suggested that whichever gap filling method is applied, the separated EMD timescales will display a distorted temporal structure of the continuous time series. As a consequence, monthly mean tide gauge sea level records were optimised by filling the gaps as best as possible using satellite altimetry data and the adjacent tide gauge records where possible, and then the oscillatory timescales of variability were separated using the EMD method with the intent to determine their physical drivers. However, identifying a single driver for each separated timescale is challenging due to our limited knowledge of how sea level is linked to the various forcing mechanisms. Therefore, the timescales of sea level variability extracted using the EMD were grouped into sub-annual and interannual timescales, and their relationship to possible driving mechanisms was investigated. The sub-annual timescale indicates how sea level responds to the mesoscale and synoptic weather systems in the annual cycle, including seasonal and annual large-scale wind and atmospheric pressure pattern changes. The interannual timescale indicates an association with the climate indices including El Niño-Southern Oscillation, Indian Ocean Dipole and Southern Annular Mode through large-scale sea surface temperature patterns and large-scale pressure and wind patterns. In addition, the results have suggested that the studied coastal sea level has an association with the Agulhas Current at both sub-annual and interannual timescale through absolute dynamic topography variations at the Agulhas Current core locations. However, due to limitations in Agulhas Current data, the study was limited to East London and Port Elizabeth and the results suggested that the Agulhas Current contribution is responsible for over 62% of the monthly sea level variability at East London. However, the results were not sufficiently consistent to suggest a firm conclusion at Port Elizabeth.

Includes bibliographical references. / Southern Africa is subject to high inter annual rainfall variability and the factors influencing southern African rainfall are not fully understood. The variability has been linked with various sea surface temperature anomalies (SSTAs) in each of the three major ocean basins as well as variability in the strength and position of regional atmospheric features. One of the atmospheric factors that may play a substantial role in southern African rainfall variability is the Botswana high, a high pressure cell which exists at the 500hPa level and is centred over central Namibia and western Botswana during austral summer. 20th Century reanalysis data is used to further investigate this feature and analysis reveals an association between the strength of the Botswana high and ENSO. Further analysis indicates that a connection between the Botswana high and rainfall over southern Africa not only exists during ENSO years, but is also apparent during neutral years that display ENSO-like characteristics in the Botswana high. This result may assist in producing better rainfall forecasts for non-ENSO years. The frequency of dry days over southern Africa during austral summer is investigated using GPCP observational data. Correlation analysis is generally in agreement with previous studies and showed that dry day frequency(DDF) over the Limpopo and North East Zambia regions is correlated with ENSO, while DDF over coastal northern Angola and central South Africa is correlated with SSTs in the Indian and Atlantic Oceans. The possible role played by DDF during JFM 1998 and JFM 2010 is investigated and results indicate that the distribution of DDF over southern Africa was notably different during these two seasons and may have contributed to the unexpected rainfall experienced over southern Africa.

Includes bibliographical references. / Linking variability in optical signals with phytoplankton community characteristics is important to extend the use of the vast resource that is the satellite ocean colour archive. Detection of species, functional types or size classes has been addressed through a spectrum of empirical to analytical approaches. A key step in developing these techniques is quantifying the sensitivity in reflectance, which can be attributed to phytoplankton characteristics (e.g cell size) under different optical regimes. Ultimately, highly spatially and temporally resolved information on phytoplankton characteristics can help the global scientific community to answer important questions relating to primary ecosystem variability. In the southern Benguela, Harmful Algal Blooms threaten public health and the economic viability of fishery and aquaculture industries in the region. Concurrently, the dominance of phytoplankton biomass amongst optically significant constituents in the southern Benguela makes the region ideal for assessing the extent to which phytoplankton characteristics beyond biomass can influence the ocean colour signal. A forward and inverse approach is presented. Phytoplankton absorption and back scattering are generated from a phytoplankton particle population model coupled to two radiative transfer approaches: a reflectance approximation and the radiative transfer model, EcoLight-S. Non-linear optimisation inversion schemes are then implemented. A simulated dataset is created to investigate how much variability in reflectance can be associated with changes in phytoplankton cell size in different bio-optical water types. This dataset is inverted to investigate the errors inherent in the inversion process as a result of ambiguity. Comparison of the two radiative transfer techniques allows for consideration of the suitability of approximations for bidirection-ality and subsurface propagation. The inversion algorithm is then applied to hyperspectral in situ radiometric data to provide validation and further assessment of errors from all sources. Results indicate that size related sensitivity in reflectance is highly dependent on phytoplank-ton biomass, as determined by the relative phytoplankton contribution to the Inherent Optical Property budget. The algorithm is finally applied to ten years of MERIS data covering the southern Benguela. A time series of biomass and cell size is presented and metrics developed to demonstrate the utility of this approach for identifying previously unobserved interannual variability in Harmful Algal Blooms.

Includes bibliographical references (leaves 153-[169]). / The objective of this study was to quantify the lateral export of organic carbon from the continental shelf of the southern Benguela upwelling system to the open ocean. The flux is potentially important because the Benguela is one of the most productive and biogeochemically active ecosystems in the global ocean. Furthermore, a significant fraction of oceanic carbon storage is modulated through the biological pump mechanism, and on millennia 1 timescales the global ocean regulates atmospheric concentrations of carbon dioxide. The current study builds on previous work, and examines both the physical and biogeochemical aspects of the lateral carbon flux from the southern Benguela. Multiple physical mechanisms capable of inducing cross-shelf advection were examined, including dynamic interaction with Agulhas Rings and upwelling front instability, however the bottom boundary layer (BBL) was the focus.

A great deal of attention has been paid to the inter-ocean exchange of thermohalineproperties in the Agulhas Retroflection region. Recent observations have shown thatthe highly energetic field of the southern half of the Cape Basin consists of bothcyclonic and anticyclonic eddies. These eddies interact with each other, resulting inthe vigorous stirring of these water mass. Investigations have shown that the cycloniceddies tend to be smaller and outnumber the anticyclonic rings. Nonetheless, verylittle is known of their characteristics and the nature in which they are formed. Usingremote sensing data, confirmed with hydrographic data, this study determines thelocation, frequency and seasonality of cyclonic eddy formation; their size, trajectoriesand lifespan; physical components and associations with Agulhas Rings.Cyclonic eddies were seen to split, merge and link with other cyclonic eddies, withsplitting events creating child cyclonic eddies. The 105 parent and 157 child cycloniceddies identified during this study show that an average of II parent and 17 childcyclonic eddies were formed annually. 31.58 % follow an overall west-southwestdirection, with 27.37 % translocating west north-westward. Poleward translocationspeeds average at 0.3 kIn/day, whereas translocation speeds obtained from alldirectional components averages at 2.153 kIn/day for parent and 2.975 km/day forchild cyclonic eddies. Parent cyclonic eddies lived for approximately 254 days,whereas child cyclonic eddies survived for a mean of 188 days. Of note was asignificant variation of lifespan between parent and child cyclonic eddies formed inboth the north and south of the study area. 77 % of northern and 93 % of southerncyclonic eddies were formed directly adjacent to positive sea level anomalies orAgulhas Rings, resulting in an total overall association of 82.93 % parent and 89.63 %child cyclonic eddies. Cyclonic eddy groups were seen to merge at a rate of 16.38parent and 14 child cyclonic eddies per year, whereas topography appeared to affectthe demise of 17.00 % of the investigated cyclonic eddies.Therefore this study may form a basis for further investigations into the influenceCape Basin cyclonic eddies have on the meridional transfer of heat, salt, nutrients,oxygen and carbon concentrations in the South-East Atlantic Ocean. A more in-depthstudy using model outputs and targeted in situ hydrographical data would againenhance cyclonic eddy knowledge.

Includes bibliographical references (leaves 153-[169]). / The objective of this study was to quantify the lateral export of organic carbon from the continental shelf of the southern Benguela upwelling system to the open ocean. The flux is potentially important because the Benguela is one of the most productive and biogeochemically active ecosystems in the global ocean. Furthermore, a significant fraction of oceanic carbon storage is modulated through the biological pump mechanism, and on millennia 1 timescales the global ocean regulates atmospheric concentrations of carbon dioxide. The current study builds on previous work, and examines both the physical and biogeochemical aspects of the lateral carbon flux from the southern Benguela. Multiple physical mechanisms capable of inducing cross-shelf advection were examined, including dynamic interaction with Agulhas Rings and upwelling front instability, however the bottom boundary layer (BBL) was the focus.