This body of work aims to contribute advancements towards developing globally applicable water quality retrieval models using Earth Observation data for freshwater systems. Eutrophication and increasing prevalence of potentially toxic algal blooms among global inland water bodies have become a major ecological concersn and require direct attention. There is now a growing necessity to develop pragmatic approaches that allow timely and effective extrapolation of local processes, to spatially resolved global products. This study provides one of the first assessments of the state-ofthe-art for trophic status (chlorophyll-a) retrievals for small water bodies using Sentinel-3 Ocean and Land Color Imager (OLCI). Multiple fieldwork campaigns were undertaken for the collection of common aquatic biogeophysical and bio-optical parameters that were used to validate current atmospheric correction and chlorophyll-a retrieval algorithms. The study highlighted the difficulties of obtaining robust retrieval estimates from a coarse spatial resolution sensor from highly variable eutrophic water bodies. Atmospheric correction remains a difficult challenge to operational freshwater monitoring, however, the study further validated previous work confirming applicability of simple, empirically derived retrieval algorithms using top-of-atmosphere data. The apparent scarcity of paired in-situ optical and biogeophysical data for productive inland waters also hinders our capability to develop and validate robust retrieval algorithms. Radiative transfer modeling was used to fill this gap through the development of a novel synthetic dataset of top-of-atmosphere and bottom-of-atmosphere reflectances, which attempts to encompass the immense natural optical variability present in inland waters. Novel aspects of the synthetic dataset include: 1) physics-based, two-layered, size and type specific phytoplankton IOPs for mixed eukaryotic/cyanobacteria 6 assemblages, 2) calculations of mixed assemblage chl-a fluorescence, 3) modeled phycocyanin concentration derived from assemblage based phycocyanin absorption, 4) and paired sensor-specific TOA reflectances which include optically extreme cases and contribution of green vegetation adjacency. The synthetic bottom-of-atmosphere reflectance spectra were compiled into 13 distinct optical water types similar to those discovered using in-situ data. Inspection showed similar relationships and ranges of concentrations and inherent optical properties of natural waters. This dataset was used to calculate typical surviving water-leaving signal at top-of-atmosphere, as well as first order calculations of the signal-to-noise-ratio (SNR) for the various optical water types, a first for productive inland waters, as well as conduct a sensitivity analysis of cyanobacteria detection from top-of-atmosphere. Finally, the synthetic dataset was used to train and test four state-of-the-art machine learning architectures for multi-parameter retrieval and cross-sensor capability. Initial results provide reliable estimates of water quality parameters and inherent optical properties over a highly dynamic range of water types, at various spectral and spatial sensor resolutions. It is hoped the results of this work incrementally improves inland water Earth observation on multiple aspects of the forward and inverse modelling process, and provides an improvement in our capabilities for routine, global monitoring of inland water quality.

The hake bottom trawl division is the largest component of the fishing industry in South Africa and it is one of the strong pillars of the food industry and the national economy. It is the main source of livelihood for many people in the West Coast and as such, finding ways of advancing it towards the direction of fourth industrial revolution is at the top of societal interests and a top priority for the major companies that are key players in the industry. Sea Harvest Group Limited is one of these key players and as such, it has undertaken to be a part of the study to improve predictability of fishing by collecting data which will contribute towards the scientific study of the patterns which determine the viability of some fishing locations over the others at different times under various conditions. The studied region is the West Coast grounds located in the southern Benguela at grid (32°S: 34°S, 16°E :19°E). The study is based on the hypothesis that the main driver of the availability of hake is the upwelling, separated into its coastal Ekman transport and curl-driven components. These two components of upwelling are driven by winds and they are known to stimulate primary production and support a larger marine food web. The correlations between these upwelling types and the mean monthly catch per unit effort (CPUE) of this region is assessed. The relationship between chlorophyll abundance and hake CPUE hypothesises lagged association of hake abundance to the underlying biological food chain driven by the upwelling events. A multiple regression model is then produced as a basic step towards quantification. The results suggest that Hake CPUE is lag correlated with upwelling and that some degree of predictability can be derived from the observation of combined upwelling patterns.

Sea-ice drift in the Antarctic marginal ice zone (MIZ) was investigated using an array of five drifting ice buoys, deployed during the winter sea-ice expansion, in July 2017. An initial 15- day analysis of pancake ice drift is presented, using the cluster of buoys, which shows: (1) exceptionally fast ice drift speeds and increased meandering of the buoys during cyclone activity; (2) high correlation of drift velocities with the surface wind velocities, even at 100% remotely sensed ice concentration, indicating free drift conditions where ice drift is primarily governed by wind; and (3) the presence of a clear energy peak (»13.5 hour period), which is suggested to be excited by the passage of cyclones through the transfer of momentum from wind. Additionally, one of the buoys (buoy U1) drifted for approximately four months from the South Atlantic sector to the Indian Ocean sector of the Southern Ocean. The analysis of this buoy revealed that it remained within the MIZ even during the winter ice expansion, as the mixed pancake-frazil field was maintained. This allowed for a continued assumption of free drift conditions for buoy U1's full drift, where it continued to respond linearly to the momentum transfer from surface winds. The analysis of buoy U1 also indicated a strong inertial signature at a period of 13.47 hours however, the wavelet analysis indicated majority of the power remained within the lower frequencies. This strong influence at the lower (multiday) frequencies has therefore been identified as the primary effect of atmospheric forcing. When these lower frequencies were filtered out using the Butterworth high-pass filter it allowed the inertial oscillations to become more significant within the wavelet power spectrum, where it can be seen that these inertial oscillations were often triggered by the passage of cyclones. The initiation of inertial oscillations of sea ice has therefore been identified as the secondary effect of atmospheric forcing, which dominates ice drift at sub-daily timescales and results in the deviation of ice drift from a straight-line path. This comprehensive analysis suggests that the general concentration-based definition of the MIZ is not enough to describe the sea-ice cover, and that the MIZ, where ice is in free drift and under the influence of cyclone induced inertial motion, and presumably waves, can extend up to »200 km.

Rainfall over southern Africa experiences substantial temporal and spatial variability which heavily impacts poor rural populations in the region that rely on rainfed agriculture for their livelihoods. Instead of totals, seasonal rainfall is better characterised by wet and dry events occurring within rainy seasons as knowledge of the frequency of such events is able to inform agricultural activity. Dry spells (pentads having <5 mm) and moderate wet days (10-30 mm) over southern Africa were assessed using high resolution (0.05◦) Climate Hazards group Infrared Precipitation with Stations (CHIRPS) datasets over the period 1981/82-2018/19 during October-November (ON), December-February (DJF) and March-April (MA) using climatology, intensity-frequency and trend analysis. Correlations with SST over the tropical southeast Atlantic and climate modes namely, El Nino Southern Oscillation (ENSO), the Subtropical ˜Indian Ocean Dipole (SIOD) and Southern Annular Mode (SAM) were computed. These, together with regressed atmospheric and SST fields were used to identify possible mechanisms for changes in dry spell and moderate wet day frequencies during austral summer. Two strong gradients in dry spell frequency were found to be present during DJF, one diagonal along the western margins of the Kalahari desert and the other meridional, lying across 20-24◦S. Topographic influences on rainfall were observed near the Drakensberg and Chimanimani mountains, Mulanje massif and Madagascan highlands where dry spell frequency (DSF) (moderate wet day frequency (MWDF)) tended to be relatively lower (higher). A region which frequently experienced half of the season as dry was identified lying across 22-24◦S (18-25◦S) during DJF (MA), with a core in the central Limpopo River Valley where 85-100% (100%) of the seasons were dry for half the season. DSF and MWDF trends indicated that drying has occurred over central South Africa during ON whereas decreasing DSF and increasing MWDF trends pointed to a weakening diagonal and meridional gradient during DJF. Additionally, increasing MWDF trends over important agricultural areas have occurred during DJF. Trends over central South Africa, part of the diagonal gradient, were associated with changes in ENSO, SAM, the Botswana High and SST in the SE Atlantic whereas those in the western Botswana region, part of the meridional gradient, were associated with those in the SIOD, Mozambique Channel Trough and Mascarene High and SST in the eastern and western Pacific.

Bibliography: p. 111-115. / The objective of this thesis was to utilise high resolution satellite data, from the NOAA AVHRR and OrbView-2 SeaWiFS sensors, to investigate the upper layer dynamics of the Benguela ecosystem in more detailed space and time scales than previously undertaken. The standard for SeaWiFS bio-optical algorithms and processing parameters are not ideal for the highly productive Benguela waters. Hence, a detailed investigation was undertaken, and the processing parameters modified for more optical application to Benguela waters. Examination of the individual radiances used in the bio-optical algorithm revealed that constituents, other than chlorophyll, were at times contributing significantly to the in-water light field. The approach adopted in this thesis was that the application of satellite data to Benguela waters should be considered either as qualitative, for event scale phenomena, or quantitative, for the longterm study.

The south coast of South Africa is a very dynamic, productive, high energy environment and is considered to be a generally challenging setting for in-water aquaculture. One of the largest environmental threats to aquaculture are harmful algal blooms (HABs), a natural ecological phenomenon often accompanied by severe impacts on coastal resources and local economies. There is a wide variety of potentially harmful blooming species in the region, with impacts resulting from both toxicity and the negative effects associated with high biomass. While HABs are fairly well documented around the southern Benguela area, the primary concern is the lack of long-term data showing if blooms are becoming more frequent, persistent or are having greater impact over the last decades, consistent with environmental change experienced in the region. For this study, high-resolution satellite remote sensing observations from 16 years of MODIS-Aqua (1 km) and one month of Sentinel-3 OLCI (300 m), using regionally optimised blended algorithms, were used to investigate the spatial distribution and temporal variability of chlorophyll-a (Chl-a) along the south coast of South Africa. A Chl-a threshold of 27 mg m−3 was used as an analytic to identify the occurrence of high biomass blooms in the remote sensing data. Phytoplankton count data from aquaculture farms are used to provide information corresponding to changes in phytoplankton community structure, and to investigate the distribution and seasonal trends of HABs along the south coast. To further explore the spatial and temporal distribution, phytoplankton species considered harmful for this study were identified and classified to their seasonal occurrence: some species were consistently present throughout the years, however each region showed contrasting seasonality. A second interest of this study is linked to assessing the capacity of the aquaculture industry to make profitable use of existing observational and early warning tools. The impact of HABs on the environment or in aquaculture facilities can be potentially mitigated by increasing the industry awareness and early warnings of HAB development. In this regard, the Fisheries and Aquaculture Decision Support Tool (DeST) was used in order to develop short term alerts on HAB development. The EO analyses conducted here specifically use the same methods used by this DeST to demonstrate the use of this tool for historical analysis in addition to real time alerting. In order to evaluate the effectiveness of the tool and how the aquaculture farmers use the ABSTRACT information provided on the DeST, an online user feedback was generated, and distributed to all stakeholders via email

Cross-slope flow is critical for governing heat and material exchange, including pollutants and biota, between the coastal and deep ocean. This study focuses on characterizing the variability of cross-slope near-bottom flow in the DeSoto Canyon region, where the BP's Macondo well exploded in April 2010, using a multi-decadal HYbrid Coordinate Ocean Model (HYCOM) simulation of Gulf of Mexico circulation. Due to change in shelf orientation east and west of the canyon, wind-driven vertical motions are mostly related to a component of the local wind vector along an angle that may deviate from the local isobaths, with smaller deviations from the along-isobath direction to the east of the canyon and bigger departures to the west. This implies that upwelling is associated with along-isobath winds east of the canyon but shelf waves propagating from the eastern shelf, where northwesterly winds are upwelling favorable, influence cross-slope flow to the west of the canyon. Beyond the shelf break, where the Loop Current and its eddies can directly impact the depth of isotherms, the isotherms are deepened underneath the Loop Current and anticyclones but uplifted on their inshore periphery. The Loop Current also interacts with the west Florida shelf and generates a high pressure gradient that extends northward along the continental slope into the study domain. Consequently, large-scale and persistent upwelling and downwelling events take place over the continental slope of the domain. The vertical excursions mostly range from ±35 to ± 50 m for the shallow isopycnals but can reach to over ± 100 m. Most distinct upwelling and downwelling events are short duration on the order of days, however there is a significant chance for persistent events, which can be induced by either remote or direct interaction of the Loop Current and/or eddies with the slope. / A Thesis submitted to the Department of Earth, Ocean, and Atmospheric Science in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2014. / September 24, 2014. / cross-slope flow, DeSoto Canyon region, Loop Current's impact, mesoscale circulation, upwelling and downwelling, wind-driven upwelling / Includes bibliographical references. / Eric Chassignet, Professor Directing Thesis; Dmitry Dukhovskoy, Committee Member; Markus Huettel, Committee Member; Steven Morey, Committee Member; William Dewar, Committee Member.

Mode water formation has long been treated as a buoyancy flux problem; however this approach fails to explain all of the variability of mode water. A number of different approaches have been demonstrated to explain more of this variability, such as links to North Atlantic Oscillation and the Gulf Stream position. These help to add to knowledge of mode water but it is still poorly understood. According to the impermeability theorem, the potential vorticity should be largely driven at the surface. In addition to this we take new approach to PV surface forcing suggested by Thomas that the PV loss is due to both buoyancy and momentum flux at the surface. The question of the relative roles of these two processes within a numerical model is addressed. It is determined that for the models mode water the buoyancy flux is the dominant cause of PV loss from the ocean and is roughly 4 times greater in magnitude that the momentum flux in the mean. / A Thesis Submitted to the Department of Oceanography in Partial Fulfillment of the Requirements for the Degree of Master of Science. / Summer Semester, 2008. / May 20, 2008. / Surface Forcing, Momentum Flux, Buoyancy Flux, Potential Vorticity / Includes bibliographical references. / William Dewar, Professor Directing Thesis; Ruby Krishnamurti, Committee Member; Jeff Chanton, Committee Member.

The subject of localized topographic circulation has received much attention in the past, in particular Taylor columns have been extensively studied and several observations indicate their existence in the real ocean. In contrast, we study here the closed circulation created above a large scale seamount, in the absence of a mean flow, by the interaction of the eddy field with the topography. This study is based on the mean state theory of Dewar (1998) which relies in part on the downgradient diffusion of potential vorticity (PV) by eddies. Using a multilayered eddy resolving quasigeostrophic model, the eddy parameterization is directly confirmed through computation of eddy PV fluxes. The critic raised by Cummins (2000) about a spurious source of angular momentum above the anomalous topography due to the parameterization is seen to depend on the geometry of the basin. In the present case, the rectangular domain can maintain a pressure gradient torque which closes the angular momentum balance. The time variability of the circulation is characterized and interpreted in the light of the mean state theory result that bottom friction and eddy diffusivity control the circulation. A very low frequency mode internal to the topographic circulation is unraveled which is related to eddy diffusivity and PV homogenization . Interactions with higher frequency basin modes are also seen to provoke the sheddings of the circulation away from its topographic anchor. The combination of these two modes leads to different regimes. In the unstable regime, the circulation is destabilized by perturbations and shed away. In the stable regime, the circulation is stronger and remains above the topography anomaly. An anticyclonic wave with azimuthal mode number one is also observed in the numerical simulation, that is similar to observations. The observation in the Argentine Basin of a strong anticyclone above the Zapiola Drift is the main motivation for the present study. Results from the present study are compared to observations of the Zapiola Anticyclone, as well as its numerical simulation with the primitive equations model SPEM. / A Dissertation Submitted to the Department of Oceanography in Partial FulfiLlment of the Requirements for the Degree of Doctor of Philosophy. / Summer Semester, 2005. / June 16, 2005. / Diffusion, Time Variability, Potential Vorticity, Quasigeostrophy, Eddies, Topographic Circulation / Includes bibliographical references. / William K. Dewar, Professor Directing Dissertation; Christopher Hunter, Outside Committee Member; Allan J. Clarke, Committee Member; Nancy Marcus, Committee Member; Doron Nof, Committee Member.

Large amplitude internal waves are a long recognized feature of the South China Sea. Remote sensing imagery often shows the sea-surface manifestation of these waves as they radiate from the Luzon passage into the deep water of the South China Sea. In situ observations have shown that the waves occur as soliton-like coherent packets, creating short wavelength depressions in the thermocline stratification. These waves are described as nonlinear, with their steepness often exceeding a slope of 1/50. In the deep basin west of Luzon, the waves are known to reach displacement amplitudes exceeding 100 m, and persist for several days as they propagate toward China and Vietnam. The packets convert to elevation anomalies as they shoal onto the continental slope, becoming stretched into longer trains of waves. Shoreward of the continental slope, there is little previous in-situ data available for use in quantifying wave energy. Here, we examine survey data from April 2005, allowing for direct assessment of waves on the continental shelf. Measurements of internal waves from the continental shelf of the South China Sea show persistent internal wave activity even during a period of neap tides. Trains of high-frequency waves were observed at multiple locations along the shelf with amplitudes typically reaching 25% of the water depth. Timing of wave packets was not obviously modulated by the tides, and intervals between wave packets were typically 0.5 to 2 hours. Measurements of Acoustic Doppler Current velocity and estimates of wave displacement allow for estimation of wave energy. Our analysis contrasts energy estimates at two sites: the 160-m isobath near the shelfbreak, and the 70-m isobath on the continental shelf. Elevated energy levels were found at the 160-m isobath site, where the depth-integrated baroclinic energy exceeded 10 kJ m-2. In contrast, we found depth-integrated energy levels were less than 1 kJ m-2 at the 70-m isobath. The normalization of energy based on internal tide generation at the shelfbreak suggests that the 160-m isobath observations are indicative of the presence of Luzon waves, while the 70-m isobath observations are indicative of locally generated internal waves. An independent hindcast of wave activity for the survey period supports our interpretation of the results. Our analysis suggests that it is possible to use an energy analysis to identify Luzon waves from local waves on the shelf. / A Thesis Submitted to the Department of Oceanography in Partial Fulfillment of the Requirements for the Degree of Master of Science. / Summer Semester, 2007. / May 25, 2007. / Continental Slope, Continental Shelf, South China Sea, In-Situ Observations / Includes bibliographical references. / Louis St. Laurent, Professor Directing Thesis; Georges Weatherly, Committee Member; Douglas Nowacek, Committee Member.