Declining water quality, in addition to hypoxia and eutrophication, may have a significant impact on the seasonality of biogeochemical parameters throughout the mainstem of the Chesapeake Bay. The carbonate (CO2) system in the Chesapeake Bay experiences seasonal and spatial complexities and is influenced by both natural and anthropogenic variability. Although site-specific studies investigating CO2-system variability exist within the Chesapeake Bay, few studies have investigated the seasonality of the CO2-system throughout the entire mainstem. Additionally, recent comprehensive studies investigating over 50 estuaries along the East Coast of the United States suggest that estuarine systems are heterotrophic and act as sources of CO2 to the atmosphere; this current paradigm does not apply to the mainstem of the Chesapeake Bay. The research presented here will assess the net annual source/sink status of atmospheric CO2 in the mainstem, along with an evaluation of annual net community production and trophic status, which is assessed based on a mass balance of dissolved inorganic carbon (DIC). Discrete observations of DIC and total alkalinity (TA) are collected at 17 stations throughout the mainstem of the Bay on four cruises between November 2016 and July 2017. The latitudinal salinity gradient along the mainstem of the Bay results in elevated DIC and TA concentrations at the mouth of the Bay associated with inflowing Atlantic Ocean waters. Minimum concentrations of DIC and TA are associated with fresher waters, delivered mainly by the Susquehanna River, at the head of the Bay. The spatial gradients in DIC and TA are observed regardless of season. Spatial variability of the partial pressure of CO2 (pCO2) is observed throughout the surface waters of the estuary, with undersaturation of CO2 with respect to the atmosphere in the upper Bay over the complete seasonal cycle, and supersaturation with respect to atmospheric CO2 in the lower Bay during the warm seasons. The spatial and seasonal distribution of pH and saturation state of aragonite (Ω) are more variable throughout the mainstem, as the seasonality of these parameters are different in each region. The physical (air-sea CO2 exchange and mixing) and biological (photosynthesis and respiration) drivers of CO2-system seasonality is examined throughout the mainstem Bay. In the deep, northern channel of the mainstem, seasonal CO2-system variability is larger than the lower Bay regions that are more directly influenced by exchange with Atlantic Ocean shelf waters. Overall, when averaged over the 2016/2017 seasonal cycle used in this analysis, the mainstem of the Chesapeake Bay is found to be net autotrophic and a sink of atmospheric CO2.

Polynyas are large areas of open water or reduced sea ice coverage that persistently form in polar environments and often experience enhanced rates of physical, chemical, and biological processes that impact ocean dynamics on local to global scales. Polynyas that form adjacent to the coast, known as coastal polynyas, play an important role in the global carbon cycle by regulating the exchange of CO2 between the ocean and atmosphere in the high latitudes. Because of their importance to the global carbon cycle, there is a particular interest to better characterize CO2 system processes in Antarctic coastal polynyas. In this study, the inorganic carbon chemistry in three East Antarctic coastal polynyas - the Dalton Polynya, the Mertz Polynya, and the Ninnis Polynya - is investigated using a combination of ship-board water column and underway observations, remote sensing products, and model outputs. The first biogeochemical observations in the Dalton Polynya are presented, and the physical and biological controls on total dissolved inorganic carbon (TCO2) are examined. Despite the evidence of TCO2 depletion due to biological production, the surface waters of the Dalton Polynya were a weak net source of CO2 to the atmosphere during the summer survey. Satellite estimates of sea surface chlorophyll a concentration suggest that the shipboard observations were made prior to the peak of the productive season and are more likely representative of the transition between spring and summer. Compared to coastal polynyas, the rates of net community production and air-sea CO2 exchange in the Dalton polynya were relatively small.

Extreme temperature events known as Marine Heatwaves (MHW), akin to atmospheric heatwaves, have only recently received attention by the estuarine scientific community. Thus far, studies have focused solely on surface events due to scarcity of long-term subsurface data. This study investigates, for the first time, the subsurface temperature and dissolved oxygen (DO) anomalies associated with surface MHW events in a large, temperate, partially mixed estuary: the Chesapeake Bay (CB). Using over three decades (1986-2021) of in-situ data from several long-term monitoring programs in the CB (including sub daily moored measurements and monthly/bimonthly cruises along the main stem) and a global atmospheric reanalysis product (ERA5), I were able to 1) characterize the spatiotemporal structure of subsurface temperature and DO anomalies during surface MHW events on seasonal time scales, 2) identify the vertical extent of warming before and after events, and 3) examine the relative role of atmospheric heat flux in driving temperature changes during the onset and decline of events. I found that subsurface temperature anomalies associated with surface MHWs had two distinct regimes: a thermally stratified spring-summer regime, when positive temperature anomalies were only present in the upper water column capped by the surface mixed layer; and a thermally homogenous fall-winter regime, when temperature anomalies extended throughout the water column. This seasonal variability in temperature anomalies was largely consistent with a simple 1-D response to heat, sourced primarily through the air-estuary interface, and with downward heat transport and diffusion controlled by seasonally variable stratification and mixing. Moreover, DO anomalies during MHW events presented a more complex spatiotemporal structure, with notable DO decreases (1-4 mg L-1) primarily occurring in the winter and spring. While negative DO anomalies were present across the main stem of the CB, the greatest DO decreases (~5 mg L-1) were observed in the upper region of CB below the mixed layer depth. During the hypoxic season (May to September), and in April and October, negative DO anomalies were often associated with an expansion of the hypoxic zone. Additionally, I observed that subsurface temperature anomalies were elevated 5-10 days before and up to 20 days after MHW events, while surface temperature anomalies were elevated for up to 2 months before and after events. This indicates that the timescales of elevated temperatures are typically much longer than the duration of individual MHW events, and therefore should be carefully taken into consideration when assessing the impact of these extreme events in the estuarine ecosystem. Using a simple 1D surface mixed layer heat budget, I identified air-estuary heat flux as the largest driver of the onset and decline of MHW events, with latent heat flux being the dominant constituent. In the CB, concurrent low DO during MHW events and persistent high temperatures before, during, and after events can compound the impacts of MHWs on habitat, which will be further exacerbated by climate change, severely impacting this valuable estuarine ecosystem.

A survey was undertaken in the southwest Indian sector of the Southern Ocean, at a fracture zone situated within the South-West Indian Ridge (SWIR). The fracture zone, formally called the Andrew Bain fracture zone (ABFZ), is centred at 50°S;30°E. The main focus of this investigation, which was strategically located around the ABFZ, was to study the dynamics and the structural modification of the Antarctic Circumpolar Current (ACC) when it encounters the complex SWIR. High sea surface variability has been observed at the southwest Indian sector of the Southern Ocean, specifically at and around 50°S;30°E. As the strong eastward flowing ACC encountered the elevated and complex bottom topography of the SWIR it was obstructed and deflected from its pathway and forced to flow through the ABFZ (50°S;30°E). Consequently the ACC was significantly narrowed at the fracture zone and immediately widened after it had flowed through the fracture zone. Its structure, therefore, was modified upstream of the ABFZ prior to entering the fracture zone, and was modified further downstream of the fracture zone. The fronts observed were the northern and southern branches of the Subantarctic Front, namely the northern Subantarctic Front (SAF), the southern Subantarctic Front (SSAF) and the Antarctic Polar Front (APF). Firstly, the SAF was occasionally encountered at the north of the survey grid, secondly, the SSAF was found to be highly variable with extreme meandering patterns across the survey grid; and lastly the APF which was observed along the 51 °S latitudinal band with minor northward and southward meanders. The SSAF and the APF partially converged at 50°30'S; 30°E, that is, at the position of the ABFZ. Coincidentally, at the same location, maximum surface geostrophic velocities of >25 cm/s were observed. The geostrophic velocities tended to be high at the vicinity of frontal bands, particularly at the convergence of the SSAF and the APF. The ACC was therefore, found to undergo structural modification, both zonally and meridionally, upstream and downstream of the ABFZ as a result of the constriction. Nutrients and dissolved oxygen (DO) had a defined distribution pattern: a decrease southwards and downwards within the survey grid. Maximum and minimum nutrients and DO were recorded south and north of the APF, respectively. Four water masses were encountered firstly the Subantarctic Surface Water (SASW), which was clearly defined north of the SSAF only upstream of the ABFZ, secondly the Antarctic Intermediate Water (AAIW) which was characterised by a salinity minimum (34.2), thirdly the Antarctic Surface Water (AASW) which was characterised by a temperature minimum of 2°C at 200m depth mainly located south of the APF in the Antarctic Zone (AAZ). Lastly, the Circumpolar Deep Water (CDW) which was the only present deep water due to the data limitations. The interaction and mixing between these water masses was evident particularly at the ABFZ. The circulation pattern of the ACC was observed to be controlled by the bottom topography. The conservation of vorticity generated latitudinal mesoscale meanders and cyclonic (cold) and anticyclonic (warm) eddies. Elevated surface velocities of >60 cm/s were observed at the ABFZ and at regions closer to the frontal bands.

A methodology for the comparative assessment of estuarine health over a range of systems is presented. It is based on the assumption that anthropogenic impact is the causative variable when considering negative impacts on estuarine health. The methodology follows a logical cascade of estuarine health assessment protocols. The first step in the Threat and Cascade Method (TaCM) incorporates socio-economic to produce a scaled indicator used to identify estuarine systems that are potentially threatened by anthropogenic inputs. The socio-economic algorithm incorporates the following variables: land cover, population density, per capita wealth, state of the estuarine mouth, abstracted mean annual runoff, encroachment of development, estuary use, and sewerage input. If the Socio-Economic Threat Index identifies the estuary as being threatened, then the second stage of the TaCM is initiated. This is an assessment of the system's physics and is accomplished by considering the following variables: residence time, estuary number (freshwater inflow/ tidal prism), coastal exchange, and the proportion of the time the estuary mouth is closed to the ocean. The Threat and Cascade Method assumes that an anthropogenically threatened system with a short residence time is less likely to be impacted on than a threatened system with a long residence time. If the Physical Threat Index identifies the estuary as being threatened, then the third stage of the TaCM is initiated. This involves assessing the chemistry and then the biology of the threatened estuarine system. The TaCM was tested using both local (South African) and international case studies. The results showed that the TaCM has the potential to become a universal methodology. The results also showed that the TaCM allows estuarine researchers and managers to rapidly assess the 'health' of a number of systems, as it mainly concentrates on estuaries that are likely to be impacted upon. The TaCM assessment identifies 'what' is causing the estuary's health to deteriorate, therefore identifying the problem areas that need to be addressed in order to mitigate the impacts on the estuary. This will allow managers to assess the success of remedial action on the estuary. The results also revealed that the TaCM could be used to predict what impact 'change' in the estuary catchment would have on an estuary's health.

The terminal region of the Agulhas Current south of Africa is characterized by the complete retroflection of the Current. The region has been shown to be populated by a range of eddies and rings. It has been observed that the spawning of an Agulhas Current ring at the retroflection is preceded by the northward wedging of the Subtropical Convergence (STC) through the retroflection loop to effectively "pinch" off these rings. The resultant entrainment of cold Sub-Antarctic Water Surface (SAASW) behind the displaced STC is of climatic and oceanographic interest in light of the concurrent interruption and eastward retreat of the warm Agulhas Current. The leakage of Agulhas Current water into the South-eastern Atlantic Ocean in the form of filaments may also be temporarily terminated during these SAASW intrusion episodes. In order to investigate intrusions of SAASW into the Agulhas Retroflection region, all available data of any kind have been accessed and analyzed. A serial satellite study, using both METEOSAT and NOAA images, suggests that approximately four intrusions of SAASW are observed per year. These intrusions generally occur between 11° E and 19° E; the westerly intrusions being more prevalent during extreme episodes of SAASW intrusions. The mean temperature and salinity distribution at the retroflection shows that the longitudinal location of SAASW intrusions seems to be geographically invariant suggesting a possible topographic influence by prominent geographical features. Hydrographic analysis of sub-Antarctic water intrusions leads one to believe that they are not just shallow, short-term phenomena but may reach to depths of approximately 800 m to 1000 m, persisting for about 28 days on average. These intrusions introduce low temperature, low salinity (< 35) water into the retroflection region with an average areal geographical coverage of 158 000 ± 118 256 km2. This suggests that these sub-Antarctic water intrusions may have important oceanographic and biologic implications to the dynamics of the Agulhas Retroflection and the oceanic region to the west of it in light of the sheer magnitude of the amount of water involved.

Unlike the rest of South Africa, the southwestern Cape (SWC) experiences most its rainfall in the austral winter (May-September). Due to interannual, intraseasonal and interdecadal variability, drought is a familiar occurrence. The SWC recently suffered from an extended dry period, known as the ‘Day Zero Drought' during 2015-2018, where greater Cape Town nearly ran out of piped water supply. Despite most rainfall in the SWC occurring from MaySeptember, considerable rainfall events have been known to occur during the summer (October-March). Such events could play a substantial role in mitigating winter droughts and multiyear droughts the region suffers from. Large Rainfall Events (LREs) during the summer of 2018/19 caused average dam levels in all major dams of the SWC to increase by more than 1%. The dam level increase is significant during the driest period of the year where dam levels decrease by several % per month. This study investigates all LREs during the summer (October-March) from 1979-2019 and their effects on major dam levels. Most summer LREs are found to be linked to atmospheric rivers (ARs) or cut-off lows (COLs), which together account for up to 88% of the top 75 LREs. Apart from one study characterising the considerable effect of ARs on winter rainfall, to date little research on ARs has been done for the region. Furthermore, COLs have been suggested to occur mostly during transition seasons. This thesis reveals that although ARs last shorter than COLs and lead to a smaller area receiving rainfall in the SWC, they both yield intense rainfall amounts with ARs concentrated around Greater Cape Town. After LREs have occurred, average dam volumes were shown to increase by up to 5% making LREs essential in drought recovery. Anomalously wet summers, which typically contain more LREs than average, are also mostly associated with cooler temperatures and less extreme hot days (90% decile). Rainfall totals are inversely correlated (r=-0.44) with extreme hot days. In addition, extreme hot days also show a significant increasing trend of 2.8 days/decade from 1979-2019. Along with increased cloud cover, weaker winds over dam catchment areas can be associated with 4 out the 5 wettest summer seasons. Of the 5 wettest summer seasons, only one (2013/14) occurred in the last two decades. Anomalously cool and wet summers, reduce the water consumption impact on dam volumes as well as help reduce the impacts of drier than normal winter seasons. Wet and cool summer seasons also reduce fire risk in the region which is important considering that the region is agriculturally productive and has experienced several devastating fires in recent decades, both in agricultural areas as well as in greater Cape Town. Although the extended summer contributes only about 30% of the year's annual rainfall, summer LREs occur during the most water demanding part of the year. Notably, increased summer LREs usually correspond with anomalously wet summers. This thesis finds that anomalously wet summers can be characterized by increased rainfall days which are linked to increased cyclonic anomalies over the region and westerly moisture fluxes shifted anomalously equatorward in the South Atlantic. These changes in circulation patterns are found to be linked to a negative Southern Annular Mode pattern and in the late summer, also linked to ENSO and the zonal wave number 3 pattern. Overall, trends suggest decreases in rainfall days in the Greater Cape Town region and in the nearby mountain areas where most major dams are located for the mid to late summer (December-March). These decreases in rainfall days can be related to poleward expansions of the South Atlantic High Pressure (SAHP) which then lead to decreases in storms impacting the SWC. With storm tracks occurring further poleward due to moisture corridor shifts and SAHP poleward expansions during recent years, there is a decrease in summer LREs in the SWC. Some of these poleward shifts are related to the tendency of the Southern Annular Mode to be in positive phase in recent decades. Since summer LREs are important in mitigating droughts in the region, future work needs to consider rainfall in all seasons rather than just the historical focus on winter rainfall which has been relatively well studied. This thesis shows the potential importance of anomalously wet summers as essential contributors to moisture in the region during the driest period of the year.

Unlike well-characterized regions that have emerging pH and carbonate data, distant areas like polar oceans remain seasonally undersampled. Consequently, there may be a significant gap in our understanding of biological implications of future ocean acidification (OA). This study seeks to examine the seawater state conditions of the carbonate system that are currently experienced by marine organisms that depend on pH and Aragonite saturation (ΩAr) for calcification. The main focus was on how the physical and carbonate characteristics are sensitive to seasonal variability in the S.E Atlantic sector of the Southern Ocean. We analyzed the temperature, salinity, Dissolved Inorganic Carbon (CT), alkalinity data (AT), pH and Omega (ΩAr) at the surface and in the upper 1000m. We then compared the seasonal meridional gradients in the surface layer and in the upper 1000m water column. The CT and AT were measured using a VINDTA instrument while pH and ΩAr were derived using the CO2SYS program. The initial hypothesis was that the southernmost part of the Southern Ocean would acidify more in winter than in spring. This was based on the idea that colder waters hold more CO2. However, we found remarkable results showing that the surface CT was consistently higher in spring than in winter, with mean seasonal differences ranging from 5.86-21.90µmol/kg although SST was consistently higher in spring than winter, with mean seasonal differences ranging from 0.67-2.12˚C within the ocean front boundaries. It was then hypothesized that the temperature, biological production and CO2 flux seasonal cycles may have been out of phase. Consistent with the CT gradient, the surface pH and ΩAr were ±0.05 units lower in the warmer waters of spring and comparatively higher in winter. The seasonal lag was seen even within the interior layers of the column. There were three main findings in this study: Firstly, since the biogeochemically controlled seasonal CO2 seasonal transition variability lagged the heat flux influence on SST, the expected winter and spring seasonal conditions for carbonate were not reflected in the timing of the winter and spring cruises. Secondly, we observed an uncoupling of pH and ΩAr surface meridional gradients. While pH had no significant meridional gradient trend apart from frontal variability, ΩAr followed the meridional trend that was driven by CT. This was due to the impact of the meridional temperature gradient on K2 that compensated for the impact of the CT gradient on the pH. Lastly, we found that the impact of the seasonal cycle of carbonate stretched down to 1000 m and it was attributed to physical processes. Our findings led us to infer that from a carbonate perspective, the winter cruise was in fact the tail end of autumn while the spring cruise was the tail end of winter.

Retrieving the optical properties of Southern Ocean (SO) phytoplankton with high confidence is critical to understanding the role of the Biological Carbon Pump (BCP). Satellite-based ocean colour remote sensing radiometry is the only observational capability that can provide synoptic views of upper ocean phytoplankton characteristics, at high spatial and temporal resolution of approximately 1 km globally, and a daily temporal resolution over a period of years to decades, as is required for climate studies. In many cases, these are the primary systematic observations available for chronically undersampled marine systems such as the SO. Inversion algorithms are applied to satellite radiometry with the goal of characterising the optical properties of the in-water constituents, primarily phytoplankton. If the relationship between Inherent Optical Properties (IOPs) and biophysical phytoplankton assemblage characteristics, in terms of abundance, cell size and pigment composition, is well understood, biogeochemical information can be inferred from satellite-derived phytoplankton IOPs. This approach has greatly augmented global comprehension of climate change and the carbon cycle. The SO is typified by unique phytoplankton optical properties, distinct from those elsewhere in the world. Most notably among these is displaying characteristically “depressed” phytoplankton absorption spectra. It is understood that there are two main drivers behind this: unusually large cell sizes, and elevated pigment density resulting from physiological changes in response to the often low light environment (photoacclimation). The primary aim of this study is to investigate the observed seasonal variability in measured in situ SO IOPs, in conjunction with the UCT-CSIR1 Equivalent Algal Populations (EAP) model of phytoplankton optical properties, to better understand the causal drivers of the optical differentiation of SO phytoplankton absorption. The EAP model is used to illustrate the biophysical source of the observed unique absorption characteristics, showing that the flattening of the spectra is driven primarily by photophysiological changes occurring during photoacclimation, namely increased density of intracellular chlorophyll a. The satellite-derived OC-CCI2 phytoplankton absorption product, observed to reproduce elevated spectra more typical of other oceans, is investigated to determine this. The model is then used to simulate biophysically consistent phytoplankton backscatter, in order to investigate whether photoacclimation, resulting in the distinctive absorption properties of the SO, has any impact on phytoplankton backscatter and the magnitude of its contribution to the bulk water-leaving signal. A reduction in phytoplankton backscatter signal was demonstrated by the model. Discussion was made in the context of opportunities for the detection of constituent IOP retrievals and biogeochemical parameters from satellites in space.

Numerous physics are responsible for forward energy cascade at oceanic fronts but their roles are not fully clear. This dissertation investigates wind-sheared turbulence in the ocean surface boundary layer (OSBL), internal wave interactions in the ocean interior, and instability-driven turbulence in energetic jets; with attention paid to the parameterizations used to quantify them. At the OSBL, meteorological forcing injects turbulent kinetic energy (TKE), mixing the upper ocean and rapidly transforming its density structure. In the absence of direct observations or capability to resolve sub-grid scale turbulence in ocean models, the community relies on boundary layer scalings (BLS) of shear and convective turbulence to represent this mixing. Despite the importance of near-surface mixing, ubiquitous BLS representations of these processes have been under-assessed in high energy forcing regimes such as the Southern Ocean. Glider microstructure from AUSSOM (Autonomous Sampling of Southern Ocean Mixing), a long-duration glider mission, is leveraged to show BLS of shear turbulence exhibits a consistent bias in estimating TKE dissipation rates in the OSBL. In the interior, finescale strain parameterization (FSP) of the TKE dissipation rate has become a widely used method for observing mixing, solving a coverage problem where only CTD profiles are available. However there are limitations in its application to intense frontal regions where adjacent warm/salty and cold/fresh waters create double diffusive instability. Direct turbulence measurements from DIMES (Diapycnal and Isopycnal Mixing Experiment in the Southern Ocean) and AUSSOM are used to show FSP can have biases of up to 8 orders of magnitude below the mixed layer when physics associated with T/S fronts are present. FSP often fails to produce reliable results in frontal zones where temperature-salinity (T/S) intrusive features contaminate the CTD strain spectrum, as well as where the aspect ratio of the internal wave spectrum is known to vary greatly with depth (as in the Southern Ocean). We propose that the FSP methodology be modified to include a density ratio-based data exclusion rule to avoid contamination by double diffusive instabilities in frontal zones. At energetic frontal jets, symmetric instability (SI) has gained momentum for explaining enhanced turbulence. Submesoscale frontal instabilities are well-established by idealized analytical and numerical studies to be a significant source of TKE in the global ocean. However, observations of TKE dissipation enhanced by SI are few, and it is unknown to what order in the real ocean this process is active. AUSSOM measured elevated TKE dissipation rates throughout the core of the Polar Front (PF). Motivated by this finding, we use a 1-km Regional Ocean Modeling System hindcast to investigate the role of SI in energy cascade and Southern Ocean mixing. We extend popular overturning instability criteria for application to ageostrophic flows. SI of the centrifugal/inertial variety is widespread along the northern continental margins of the Antarctic Circumpolar Current due to topographic shearing of the anticyclonic side of PF-associated jets but is notably absent (above 1-km scale) from the open-ocean mixed layer. Contrarily, modeled velocity fields are strongly indicative of critical layers and other internal wave interactions dominating the open-ocean elevated TKE budget even at energetic fronts.