Submarine canyons can impact regional oceanography and provide a conduit for shelf-slope exchanges via topographically induced processes such as canyon upwelling and downwelling. Between Virginia and New York in the Mid-Atlantic Bight (MAB), there are five major shelf-incising canyons (Norfolk, Washington, Baltimore, Wilmington, and Hudson canyons) and four sizable slope-confined canyons (Accomac, Spencer, Lindenkhol, and Toms canyons). Canyon upwelling and downwelling at these canyons have not been well studied. Consequently, the associated hydrographic variability and dynamics inside the canyons and on the adjacent shelf are largely unknown, and the integrated impact of submarine canyons on MAB shelf hydrography and shelf-slope exchanges is poorly understood. This dissertation was inspired by a glider-based survey at Wilmington Canyon, and mainly used numerical modeling simulations for the MAB with an unstructured-grid three-dimensional ocean model to answer these questions. Using glider observations and realistic numerical modeling for February 25–March 7, 2016, Chapter 2 investigated the hydrographic variability associated with the Wilmington Canyon and adjacent outer shelf and shelf-break amid two consecutive events of upwelling and downwelling. Then focusing on the same Wilmington Canyon upwelling and downwelling events and using a realistically forced numerical modeling simulation as well as one without tidal forcing, Chapter 3 tested the dynamical drivers of winds and tides in canyon upwelling and downwelling events, also compared the differences in dynamics between the canyon and adjacent shelf-break. Chapter 4 presented the occurrences and integrated impact of 12 cycles of spatially coherent upwelling and downwelling through nine canyons between Virginia and New York, based on a realistic numerical modeling experiment and a No-Canyon experiment for January 1–April 14, 2016. Chapter 4 also analyzed the frequency of canyon upwelling and downwelling based on a 22-year record (1994–2015) of sea surface elevation. This dissertation found that the submarine canyons in the MAB induced significant spatial and temporal hydrographic variabilities on the shelf and enhanced shelf-slope water exchange. Due to favorable winds, sea surface tilts, and shelf-scale background ocean currents, as well as canyon topography, cycles of spatially coherent multi-canyon upwelling and downwelling frequently occurred in the MAB. Plumes of upwelled slope water from the canyons intruded the outer and mid shelf during the upwelling episodes, and dense water from the shelf retreated into the canyons during the downwelling episodes. For each cycle of upwelling and downwelling, upwelled water from the canyons caused shelf-scale anomalies of low temperature, high density, and northeastward velocity on the MAB outer shelf that were significant when averaged over the course of the season. This thesis suggests that submarine canyons are an integral part of MAB oceanography and deserve further investigations.

Algal blooms occur annually in many parts of the Chesapeake Bay. The causes of algal blooms are complex and can be different in different regions. In this study, we will conduct data analysis for the observed data and adopt various methods to investigate algal bloom phenomenon in three separate regions in the oligo/poly-haline portion of the Bay. Chapter 1 provides a general introduction of the algal bloom research in the Chesapeake Bay. In Chapter 2, an observational analysis and a numerical study on the algal blooms in Back River were conducted. A hypothesis was made that high pH can trigger sediment phosphorus release, which in turn can enhance chlorophyll-a and further increase pH to form a positive feedback loop. to test this theory, water quality model ICM coupled onto SCHISM was applied in Back River to study the phenomenon. Moreover, a pH model was developed to describe the aquatic chemistry. The model results with and without pH model were compared with Bay Program observations for verifying our hypothesis. It proves the importance of sediment phosphorus release on the algal blooms in Back River. In Chapter 3, a theoretical study combined with data analysis on cyanobacteria blooms dynamics was conducted in the upper tidal James River. The theory integrates the physical transport and biological effects, which leads to a simple governing equation composed of an advection term and a phytoplankton net growth term, in both linear and nonlinear forms. In this study, we derived a general analytic solution to the equation. Then, we applied the theory in the tidal freshwater portion of the James River. The theoretical predictions of chlorophyll concentrations were compared with observational data and verified the validity of the solution. In addition, the factors related to the local chlorophyll maximum in tidal freshwater rivers were discussed. In Chapter 4, an observational analysis and numerical experiments were performed to investigate the algal bloom in the polyhaline of the Chesapeake Bay. This exploratory study is aimed to explain the broad distribution of C. polykrikoides blooms in the lower Bay and the sudden disappearance of the bloom in 2014. A hypothesis is made regarding the origin of C. polykrikoides cysts. In this hypothesis, the cysts are considered to be originated from coastal ocean and their transport is under the influence of wind patterns and gravitational circulation. In this study, the hydrodynamics in the lower Chesapeake Bay was first analyzed. Then, a series of particle tracking experiments were conducted for investigating the physical transport of C. polykrikoides cysts under different environmental conditions. Finally, water quality model ICM was used to simulate the algal blooms caused by C. polykrikoides in the lower Bay by incorporating the biological features of C. polykrikoides. The model can generate reasonable magnitude of the algal blooms in 2012, 2013 and simulate no algal bloom condition in 2014.The result indicates that C. polykrikoides cysts could be originated from the coastal ocean, while temperature and wind patterns play important roles in further controlling the subsequent development of the blooms.

A least-squares inverse method was devised to estimate horizontal pressure gradients and vertical eddy-viscosity profiles simultaneously, from current profiles. The method was designed mostly for observations of deterministic or near-deterministic wave currents. Tidal-current observations were chosen for the present study. The inverse system was constructed from a linearized momentum equation. The viscosity was modeled with a time-constant and harmonic function in time, but without its vertical structure predefined. The least-squares problem was solved with the singular value decomposition, by taking current harmonic profiles as input. at first, the method was tested with current profiles simulated by a numerical model employing the mixing-length theory for vertical eddy viscosity. Analyses were done on fourteen sets of real measurements at 6 stations in Chesapeake Bay and one of its tributaries. Thirteen were from current-meter moorings, and one was from a bottom-mounted acoustic Doppler current profiler. It turned out that the proposed method performed well enough to diagnose a linearized dynamic balance which involved a friction term with time-constant, but depth-dependent eddy viscosity. Eddy-viscosity profiles appeared to have linear-exponential structure. The apparent maximum varied significantly in season, implying some stratification effect. Using the primary results, values of drag coefficient (&C\sb{lcub}d{rcub}&) and depth-average TKE production were deduced. Results of &C\sb{lcub}d{rcub}& indicated some seasonal variation of bottom roughness. Depth-average TKE production in the lower bay appeared to be &{lcub}\sim{rcub}&8 times higher than in the mid- or upper bay. The production in the upper part of the York River appeared to be 3&{lcub}\sim{rcub}&4 times higher than the lower part. Among them, the upper part of the York River appeared to have the highest production. The approach will be a good tool for the analysis of ADCP measurements in field, due to the simplicity, yet the diagnostic power. The application, however, is limited mostly to deterministic current measurements. The approach is not appropriate to strongly advective flows. Even for weakly advective flows, it is incapable of determining the oscillatory part of the viscosity successfully, due to truncated nonlinear-advective terms.

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Previous studies on severe weather in South Africa have often focused on synoptic-scale systems such as cut off lows, tropical extratropical cloud bands, and tropical cyclones, with little attention placed on the smaller mesoscale convective systems (MCSs). On a global scale, MCSs are not only important as key rainfall producers, but are often responsible for flooding, severe winds, hail and sometimes tornadoes. MCSs in South Africa remain poorly understood with there being little evidence of any long-term climatology studies of these systems over the region. A climatology of large, long-lived MCSs over eastern South Africa for the extended austral summer (September-April) from 1985-2008 is presented. On average, 63 MCSs occur here in summer, but with considerable interannual variability in frequency. The systems mainly occur between November and March, with a December peak. This seasonal cycle in MCS activity is shown to coincide with favorable convective available potential energy (CAPE) and vertical shear profiles across the domain. Most systems tend to occur along the eastern escarpment with its sharp topographic gradients close to the warm waters of the northern Agulhas Current. The eastern escarpment can act as a convective trigger by mechanically uplifting sufficiently moist and unstable air masses. In addition, strong latent heat fluxes from the northern Agulhas Current help to create high-CAPE conditions. Typically, initiation begins in the early afternoon, MCS status is reached mid-afternoon, maximum extent early in the night and termination around midnight or shortly thereafter. The analysis also considered MCSs that developed over land versus those over the adjacent ocean. It is found that most MCSs initiate over land, but systems that initiate over the ocean tend to last longer than those that develop over land. The results also show that there are differences in the seasonal cycle between continental and oceanic MCSs, with oceanic systems containing two intraseasonal peaks (December and April). There is a relatively strong positive relationship between the southern annular mode (SAM) and early summer MCS frequency. For the late summer, the frequency of MCSs appears related to the strength of the Mascarene high and Mozambique Channel trough, which modulate the inflow of moisture into eastern South Africa and the stability of the lower atmosphere over the region. The 6 results indicated that there is considerable variability in the long-lived MCS frequency on interannual time scales and such variability can have considerable impacts on regional rainfall totals during the summer months over eastern South Africa. MCSs are known to produce heavy rainfall that is often associated with floods, which can be devastating to livestock, crops, infrastructure, and humankind. However, these systems also provide important rainfall within a short time span that is significant for rain-fed agriculture for a semi-arid country as South Africa. Using Climate Hazards Infrared Precipitation with Stations (CHIRPS) satellite rainfall data for 1985-2008, this study identified 38 daily extreme rainfall events which account for 40% of the top 50 extreme rainfall events over the two sub-domains of the eastern parts of South Africa that are linked to long-lived MCSs. Of the 38 events, systems duration ranged between 6-51 hours with 23 systems lasting for longer than 12 hours. Individual MCS-associated extreme daily rainfall events contribute between 21% - 54% to the total seasonal amount of rainfall over eastern South Africa. There is also noticeable interannual variability of seasonal rainfall over the northern and the southern domain, and considerable spatial variability in seasonal rainfall of MCS-related extreme rainfall events over the two sub-domains. In general, the thesis has contributed to a better understanding of the wider group of large, longlived MCS characteristics over eastern South Africa in terms of their distribution, frequency, life cycle, seasonal cycle and large-scale environmental conditions and the relationship between MCS frequency and interannual climate mode of variability such as El Niño-Southern Oscillation (ENSO), the subtropical south Indian Ocean dipole (SIOD), and SAM. The study also contributed to a better understand the role MCSs play in eastern South Africa summer rainfall and particularly extreme rainfall in the region.

Coastal topography and more specifically, the impact of local hydrography can significantly influence phytoplankton dynamics along the California coast. In San Luis Obispo Bay California, the local hydrography is influenced by the presence of a lee and proposed upwelling shadow in the northwest corner of the bay. These conditions allow for periods of unperturbed phytoplankton growth creating phytoplankton incubation areas. Phytoplankton dynamics including accumulation, advection, and composition were examined in San Luis Obispo Bay California from January to June 2004 using all the primary techniques of ocean monitoring encompassed in the coastal module of the Global Ocean Observing System. These techniques included remote sensing, autonomous sensing, discrete sampling and laboratory analysis. Results demonstrated that composition in the bay followed the typical seasonal shifts seen along the California coast. These findings reveal a community that was primarily dominated by dinoflagellates during the winter months giving way to a diatom dominated community in the spring and summer as upwelling season reached the coast. The model of cyclic phytoplankton accumulation and advection was shown to be valid and driven by both coastal upwelling as well as poleward displacement during periods of relaxation. In addition, due to presence of a stratified subsurface chlorophyll layer, the depth component was shown to be vital when attempting to access and sample phytoplankton communities in the bay.

The Agulhas Current system is a vital part of the global thermohaline circulation. This global thermohaline overturning of the oceans has in turn an inextricable link to world climate. Although this current is so important, relatively little is known on its sources. One of these proposed sources of the Agulhas Current is the southern limb of the East Madagascar Current (EMC). Previously the EMC was primarily studied through the use of drifters, remote sensing and ships' drift methods. In an attempt to increase the understanding of this possible source region a first dedicated cruise was organised for the southern termination of the EMC. The cruise took place in March 2001. The hydrographic and other data from the cruise have the potential to describe the EMC termination in a seminal way. The EMC is shown to consist of Tropical Surface Water, Subtropical Surface Water and South Indian Central Water. In the region of the EMC Antarctic Intermediate Water, North Indian Deep Water and North Atlantic Deep Water/Circumpolar Deep Water were found. There is clear evidence of the presence of Red Sea Intermediate Water with salinities greater than 34.5 psu at temperatures between 4 and 6.5°C from 800-1250 m, inshore of the EMC. The width of the current during the cruise period was 100 km, the maximum speed of the current was 1.1 m/s and the depth of the current was 1000 m. The maximum transport of the EMC was calculated to be 39.3 Sv. An EMC undercurrent was found with a depth range of 1000-2000 m. The maximum speed of the undercurrent was seen to be 0.3 mis and the transport of the undercurrent was 0.8 Sv. No retroflection of the EMC emerges from this data set. Satellite geostrophics over a period of 13 years give evidence of eastward flow being associated with eddies in the region of the EMC termination. References have suggested that such eddies may give the appearance of a retroflection. From the observations there was ample evidence for the presence of a relatively weak upwelling cell inshore of the EMC. The temperature at the surface of the upwelling cell was 26°C (2 degrees less than the surrounding water) and the chlorophyll concentration was 0.63 mg Chl-a/m3 . Nitrate concentration was 6.4 µmol/kg at 100 m, phosphate 0.53 µmol/kg, silicate 5.69 µmol/kg and oxygen was 107.5 µmol/kg. At 45 km from the coast there was an average movement of water offshore down to a depth of 40 m. The maximum speed of the offshore flow was 0.5 m/s.

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.