Dredging is often conducted to maintain authorized depths in coastal navigation channels. Placement of dredged sediment in the form of nearshore berms is becoming an increasingly popular option for disposal. Compared to direct beach placement, nearshore berms have fewer environmental impacts such as shore birds and turtle nesting, and have more lenient sediment compatibility restrictions. Understanding the potential morphological and sedimentological evolution is crucial to the design of a nearshore berm. Furthermore, the artificial perturbation generated by the berm installation provides a unique opportunity to understand the equilibrium process of coastal morphodynamics. Matanzas Pass and Bowditch Point, located on the northern tip of Estero Island in west-central Florida were dredged in October 2009. The dredged material was placed approximately 600 ft offshore of Fort Myers Beach and 1.5 miles southeast of Matanzas Pass, in the form of an artificial berm. Time-series surveys and sediment sampling were conducted semi-annually in order to quantify sedimentological characteristics and morphological changes within the first year after construction of the berm. The artificial berm at Fort Myers Beach is composed mainly of fine sand. Patches of mud were found throughout the study area, with the highest concentrations being in the trough landward of the berm, and offshore southeast of the berm area. The highest concentration of carbonates was found in the swash zone, as well as at the landward toe of the berm, which coincides with the coarsest sediment. The overall mud content of the berm is lower than that of the dredged sediment, thus indicating a coarsening of the berm over time. The reduction in fines as compared to the original dredged sedimet could also indicate a selective transport mechanism that moves finer material offshore, and coarser material landward, a desirable trend for artificial berm nourishment. During the course of the first year, the berm migrated landward and increased in elevation. Onshore migration occurred mostly within the first 6 months. Along with onshore migration, the shape of the berm changed from a symmetrical bell curve to an asymmetrical shape with a steep landward slope. There is no clear spatial trend of volume change alongshore within the berm area, indicating that sediment transport is mostly cross-shore dominated. A salient was formed landward of the northern portion of the berm. Several gaps were created during berm construction due to dredging and placement techniques. These dynamic gaps are likely maintained by rip currents through them. This study showed that the Fort Myers Beach berm is active, due to its landward migration during the first year after construction.

Atualmente, o beijupirá é a espécie nativa que reúne o maior número de características em comum com outras espécies aquáticas cultivadas comercialmente, sendo assim, indicada para ser a espécie pioneira na piscicultura marinha brasileira. No entanto, sua criação é incipiente. Neste trabalho, foram realizados dois estudos pontuais: um para monitorar a criação de beijupirás em gaiolas, sistema offshore, no litoral de Pernambuco; e outro para monitorar a criação de beijupirás em tanques-redes, sistema nearshore, no litoral de São Paulo. O objetivo foi aferir parâmetros ambientais de qualidade da água de criação, físico-químicos e microbiológicos do beijupirá, que possam ser utilizados na elaboração de um sistema modelo de rastreabilidade da cadeia produtiva dessa espécie. Em ambos os estudos foram realizadas quatro coletas em diferentes meses do ano, com o intuito de se avaliar as possíveis correlações existentes entre os parâmetros ambientais - índice pluviométrico e temperatura do ar - e os parâmetros de qualidade avaliados na água de criação - oxigênio dissolvido, temperatura, demanda bioquímica de oxigênio, demanda química de oxigênio, salinidade, amônia, nitrito, nitrato, fosfato, carbono orgânico total, turbidez, transparência, CO2, pH, clorofila a e contagem microbiológica - e nos peixes - biometria, rendimento, composição centesimal, ácidos graxos, aminoácidos, pH, bases voláteis totais e contagem microbiológica. Verificou-se que a maioria dos parâmetros físico-químicos e microbiológicos avaliados na água de criação, estavam em conformidade com a legislação brasileira vigente ou dentro dos limites sugeridos pela literatura para criação dessa espécie. Todavia, esses parâmetros apresentaram variação nos diferentes meses de coleta, principalmente no estudo realizado no sistema nearshore, o que dificulta afirmar as possíveis interferências desses parâmetros na qualidade e desempenho dos animais. Os peixes amostrados apresentaram baixo desenvolvimento zootécnico, se comparado ao peso total final previsto na literatura para essa espécie. No entanto, o rendimento em filé apresentou-se satisfatório, principalmente no sistema nearshore, aproximadamente 40%. Todas as amostras de filés de beijupirás avaliadas apresentaram conformidade microbiológica, frescor e qualidade nutricional, principalmente no que se refere à composição dos seus aminoácidos e ácidos graxos, com destaque para presença de lisina e ácidos graxos Eicosapentaenoico (EPA) e Docosahexaenoico (DHA), sendo, estas informações úteis para efeitos de marketing na divulgação e estimulo do consumo dessa espécie. O mesmo foi observado para o resíduo gerado após o processamento dos filés, o que sugere a possibilidade de elaboração de coprodutos com qualidade nutricional, tornando a cadeia produtiva dessa espécie mais rentável e sustentável. Os alimentos fornecidos aos animais, não eram adequados para satisfazer as exigências nutricionais dos mesmos, sendo a falta no mercado de rações elaboradas com formulações específicas um entrave para o sucesso dessa atividade. Conclui-se que os parâmetros, temperatura da água de criação; rendimento em filé, destreza do filetador; quantidade e tipo de resíduo gerado na filetagem; frescor e qualidade microbiológica dos filés; assim como, composição centesimal dos filés, resíduos e alimento fornecido aos animais, especificamente composição em aminoácidos e ácidos graxos, devam ser monitorados no sistema de rastreabilidade. Quando implementado, o sistema de rastreabilidade permitirá uma tomada de decisão mais consciente a respeito das condições de criação ideais do beijupirá, no intuito de dispor respostas práticas e aplicadas ao setor produtivo quanto ao atendimento às exigências da legislação, do mercado e do consumidor final / Currently, cobia is the native species with the largest number of characteristics in common with other aquatic species commercially farmed; therefore, it is indicated as the pioneer species in Brazilian marine fish farming. However, its rearing is incipient. In this work, there were two specific studies: one to monitor cobia rearing in cages offshore on the coast of Pernambuco State, Brazil; and another to monitor cobia rearing in nearshore cages on the coast of São Paulo State. The objective was to measure farm water quality, physico- chemical and microbiological parameters of cobia that can be used in the preparation of a model system traceability of the production chain of this species. In both studies, four collections were performed in different months of the year to evaluate possible correlations between environmental parameters, such as rainfall and environment air temperature, and the quality parameters evaluated in the water rearing, such as dissolved oxygen, temperature, biochemical oxygen demand, chemical oxygen demand, salinity, ammonia, nitrite, nitrate, phosphate, total organic carbon, turbidity, transparency, CO2, pH, chlorophyll a and microbiological contamination, as well as fish, such as biometrics, yield, proximate composition, profile of fatty acids and amino acids, pH, totals volatile bases and microbiological contamination. Most of the physico-chemical and microbiological parameters evaluated in the rearing water were in line with the current Brazilian law or within the threshold suggested in the literature for rearing this kind of species. However, these parameters showed great variation for different months of collection, especially in the study conducted in a nearshore system, making it difficult to state the possible interference of these parameters on the quality and performance of the animals. The sampled fish had low livestock development, compared to growth rates reported in the literature for this species. However, fillet yield was satisfactory, especially in the nearshore system, close to 40%. All samples of cobia fillets showed microbiological compliance, freshness and nutritional quality, especially in terms of composition of its amino acids and fatty acids, mainly in the presence of lysine and fatty acids, respectively, Eicosapentaenoic (EPA) and Docosahexaenoic acid (DHA). This information can be used as an excellent marketing tool to disseminate and stimulate consumption of this species. The same was observed for the waste generated after processing the fillets, suggesting the possibility of developing by-products with nutritional quality, making the supply chain of cobia more sustainable and profitable. The feed provided to the animals was not adequate to meet their nutritional requirements, and the short supply of prepared feed with specific formulations is an obstacle to the success of this activity. We conclude that the parameters of water temperature, fillet yield, skill of take fillet, amount and type of waste generated in filleting, freshness and microbiological quality of steaks, as well as chemical composition of fillet, waste and feeding for the animals, mainly amino acid composition and fatty acids, should be monitored in the traceability system. When implemented, the traceability system regarding the decision-making process for the ideal conditions of cobia production, providing practical answers, and it can be applied to the productive sector as a way to comply with requirements of legislation, market and consumers

The ecological importance of drifting will depend on the abundance of drifting algae and whether it is reproductively viable. However, the ability of adult plants to successfully disperse long-distances by drifting is largely unknown, particularly for fucoids. The abundance, species composition, and reproductive status of drifting algae was examined by transect surveys around Kaikoura and Banks Peninsula. Abundance and species composition varied between sites, but all drifting algae that were in reproductive season, and had reproductive structures intact, were reproductively active. The reproductive longevity and viability of drifting and beach-cast Hormosira banksii, Durvillaea antarctica and Cytophora torulosa was compared with attached populations. Drifting algae remained reproductively viable, and fecundity did not differ from that of attached algae. Viable propagules were released from drifting algae for the duration of the experiments (H. banksii 57 days, D. antarctica 62 days, and C. torulosa 43 days). In contrast, beach-cast algae ceased to release propagules after 14 days. Dispersal by drifting relies on offshore transport after detachment. To determine the influence of wind and tidal currents on the nearshore transport of drifting algae, tagged H. banksii, D. antarctica, C. torulosa and GPS-tracked drifters were released from shore. Drifters generally moved in the direction of the prevailing wind, but some influence of tidal direction and bathymetry was detected. Offshore winds and outgoing tides were favourable for the offshore transport of surface drifting algae. Following dispersal and arrival at new locations, the distance between gametes may be important in determining the fertilisation success of dioecious species. Experiments testing the fertilisation success of H. banksii and D. antarctica, over increasing distances, showed that fertilisation success decreased with increasing distance between male and female gametes. Despite this, eggs were fertilised when male and female gametes were up to 2m apart, and sperm remained viable for 2 hours.

A two-dimensional numerical model has been developed to simulate wave-current induced nearshore circulation patterns in beaches and surf zones. The wave model is based on the parabolic wave equation for mild slope beaches. The parabolic equation method has been chosen because it is a viable means of predicting the characteristics of surface waves in slowly varying domains and in its present form dissipation and wave breaking are also included. The two dimensional parabolic mild slope equation was discretised and solved in a fully implicit manner, so stability did not create a major problem. This wave model was then embedded into the existing numerical model DIVAST. The sediment transport formulae from Van Rijn was used to calculate the nearshore sediment transport rate.

Approved for public release, distribution is unlimited / Rip current spacings are compared with wave energetics and directional spreading in the Southern Monterey Bay. Southern Monterey Bay affords a unique environment to study rip currents owing to their prevalence created by near-normally incident waves on a sandy shoreline. It is hypothesized that rip current spacing is a function of wave directional spreading and energy flux, based on the morphodynamic modeling by Reniers et al. 2003. A gradient of wave energy flux exists due to headlands and refraction over Monterey Canyon. Rip currents are shown to occur between cusps in the shoreline, allowing cusp spacing to be a surrogate for rip spacing. Rip current spacing was inferred from beach morphology surveys, LIDAR imagery, and Argus cameras, and found to be O(150m) at Sand City and O(300m) at Marina, separated by 6km . Measured waves during a two month period using wave-rider buoys, show a gradient of across-shore energy flux between Sand City, 2 28000( / ) F Jm x . , and Marina, 2 33000( / ) F Jm x . . The two sites have the same peak directional spreading of energy value, 14 peak ̤= o , and slightly different bulk values for Sand City, 18 bulk ̤= o , and Marina, 20 bulk ̤= o . Therefore, the variations in rip current spacing could not be attributed to directional spreading but appear related to variations in energy flux. / Ensign, United States Naval Reserve

Approved for public release, distribution is unlimited / Accurate predictions of nearshore wave conditions are critical to the success of military operations in the littoral environment. Although linear spectral-refraction theory is used by the main operational forecasting centers in the world for these predictions, owing to a lack of field studies its accuracy in regions of complex bathymetry such as steep shoals and submarine canyons is unknown. This study examines the accuracy of linear spectral-refraction theory in areas of complex nearshore bathymetry with three months of extensive wave data collected during the Nearshore Canyon Experiment (NCEX) held in the fall of 2003. The field site, off La Jolla California, is characterized by two submarine canyons that strongly affect the propagation of long period Pacific swell. Data from 7 directional waverider buoys, 17 bottom pressure recorders, and 12 pressure-velocity sensors, were examined and compared to predictions made by a high resolution spectral-refraction model. Analysis reveals large spatial variation in wave heights over the area especially in the vicinity of the canyon heads, where wave heights vary by as much as an order of magnitude over a few hundred meters. This extreme variation in wave conditions across the canyons is surprisingly well described by refraction theory with typical errors of nearshore wave height predictions of about 20 percent. / Lieutenant, Royal Australian Navy

Understanding how coral reefs have developed in the past is crucial for placing contemporary ecological and environmental change within appropriate reef-building timescales (i.e. centennial to millennial). On Australia’s Great Barrier Reef (GBR), coral reefs situated within nearshore settings on the inner continental shelf are a particular priority. This is due to their close proximity to river point sources, and therefore susceptibility to reduced water quality as the result of extensive modification of adjacent river catchments following European settlement in the region (ca. 1850 CE). However, the extent of water quality decline and its impact on the coral reefs of the GBR’s inner-shelf remains contentious and is confounded by a paucity of long-term (> decadal) datasets. Central to the on-going debate is uncertainty related to the impact of increased sediment loads, relative to the natural movement and resuspension of terrigenous sediments, which have accumulated on the inner-shelf over the last ~6,000 years. The main aim of this thesis was to characterise and investigate the vertical development of turbid nearshore coral reefs on the central GBR. This aim was achieved through the recovery of 21 reef cores (3 - 5 m in length) from five proximal turbid nearshore reefs, currently distributed across the spectrum of reef ‘geomorphological development’ within the Paluma Shoals reef complex (PSRC). The recovered reef cores were used to establish detailed depositional and palaeoecological records for the investigation of the (1) internal development and vertical accretionary history of the PSRC; and (2) compositional variation in turbid nearshore coral and benthic foraminiferal assemblages during vertical reef accretion towards sea level. Established chronostratigraphic and palaeoecological records were further used to assess the impact of post-European settlement associated water quality change in a turbid nearshore reef setting on the central GBR. Radiocarbon dating (n = 96 dates) revealed reef initiation within the PSRC to have occurred between ~2,000 and 1,000 calibrated years before present, with subsequent reef development occurring under the persistent influence of fine-grained (< 0.063 mm) terrigenous sediments. The internal development of the PSRC was characterised by discrete reef facies comprised of a loose coral framework with an unconsolidated siliciclastic-carbonate sediment matrix. A total of 29 genera of Scleractinian coral and 86 genera of benthic foraminifera were identified from the palaeoecological inventory of the PSRC. Both coral and benthic foraminiferal assemblages were characterised by distinct assemblages of taxa pre-adapted to sediment stress (i.e. low light availability and high sedimentation). At the genus level, no discernable evidence of compositional change in either coral or benthic foraminiferal assemblages was found, relative to European settlement. Instead, variations in assemblage composition were driven by intrinsic changes in prevailing abiotic conditions under vertical reef accretion towards sea level (e.g. hydrodynamic energy, light availability, and sedimentation rate). These findings therefore highlight the importance for considering reef ‘geomorphological development’ when interpreting contemporary reef ecological status. Furthermore, this research emphasises the robust nature of turbid nearshore reefs and suggests that they may be more resilient to changes in water quality than those associated with environmental settings where local background sedimentary conditions are less extreme (e.g. towards the inner/mid-shelf boundary). To this end, this thesis presents new baseline records with which to assess contemporary ecological and environmental change within turbid nearshore settings on the central GBR.

Understanding the behaviour of waves and their interaction with the coast is vital for marine engineers and maritime planners. As sea levels rise due to climate change, low-lying coastal areas and existing sea defences will become increasingly vulnerable to run-up and overtopping by large wave events. Accurate and effcient numerical models are essential tools for the assessment of such events and the impact they have on the coast so that effective coastal protection can be designed. This thesis presents a depth-integrated numerical solver with two horizontal dimensions for modelling waves in the coastal zone from intermediate depth to zero depth. Pre-breaking, the evolution of the water surface is calculated using the enhanced Boussinesq equation set of Madsen and Sorensen (1992). This equation set has improved dispersion characteristics over the classical Boussinesq equations, but with relatively few terms compared to models based on the Navier-Stokes equations, allowing for more effcient numerical modelling while maintaining suffcient accuracy. The equations are discretised using second-order finite differences and solved using the conjugate gradient method with fourth-order Runge-Kutta time stepping. Switching from the Boussinesq equation set to the shallow water equations allows shoaling waves to break, with the broken waves then propagating as bores. The shallow water equations are solved using a finite volume MUSCL-Hancock scheme with an HLLC approximate Riemann solver in order to resolve the behaviour of steep-fronted bores at the shore. The model incorporates a wetting and drying algorithm that models the moving wet/dry front. Waves are generated by a line of independently moving piston paddles, allowing full replication of laboratory experiments. A mapping technique is used in the region of the paddles to map the moving physical domain onto a fixed computational domain to facilitate the solution of the governing equations. Different aspects of the model are verified using standard benchmark tests. The complete model is then validated by comparing the numerical simulation of laboratory experiments with high quality experimental data from the UK Coastal Research Facility (UKCRF). The laboratory experiments simulated include the interaction of regular waves with sinusoidal and tri-cuspate beaches, and the interaction of both uni-directional and multi-directional focused wave groups with a plane beach. It is found that the model provides satisfactory wave phase resolution and reproduces most of the flow features of waves and currents in the shallow nearshore environment.

Shell Key and Mullet Key are two sandy barrier islands on the West Central Florida coast near the mouth of Tampa Bay. These islands are part of an interconnected barrier-inlet system that includes Pass-a-Grille (PAG) and Bunces Pass. Shell Key is a relatively new island about 40-years of age that formed in between the two inlets of Bunces Pass and PAG. Mullet Key is an island to the south of Shell Key situated between Bunces Pass and the main Tampa Bay channel that has demonstrated large scale upward shoaling events. Using numerical modeling, the wave and tidal conditions at the dual-inlet system were investigated in order to understand the hydrodynamic conditions that drive the morphology change. Historical aerial imagery and historical nautical charts were analyzed to determine the large scale accretionary and erosive changes that happened in the study area from 1873 to 2018. Four historical nautical charts, from 1873, 1928, 1966, and 1996 were digitized to create bathymetry maps of the two islands, their adjacent inlets, and the ebb shoals. These historical bathymetry maps were compared with the bathymetry survey by this study in 2016. The research goal of this thesis is to investigate the mechanism of origin and development of two barrier islands along the coast of West Central Florida through a time series of photos combined with numerical modeling. Based on aerial photos from 1984 to 2018, the overall shape and orientation of ebb shoals at both Bunces Pass and PAG were analyzed in order to examine the effect that the 30 year swash bar cycle at Bunces Pass has on a connected inlet system. The ebb shoal orientations were compared to see how swash bar initiation would affect the two ebb shoals; most notably Bunces Pass ebb shoal. A bending of the entire Bunces Pass ebb shoal was identified over the 2002-2018 time span corresponding to the development of a large sand feature located here. Further numerical modeling was conducted at PAG to determine the factors controlling the formation of Shell Key. Before the 1970s, the PAG inlet included two branches, the North PAG Channel and the South PAG Channel. A major dredging event took place at the North PAG Channel in 1966 causing significant widening and deepening of the channel. This dredging event was simulated to quantify the impact to the natural flow pattern. The 1966 dredging project had a significant impact to the overall flow pattern, increasing the ebb jet flow velocity by 0.8 m/s over the dredged area and significantly decreasing flow velocity by -0.4 m/s over a large area where the South PAG Channel was previously located. This artificially induced change of flow pattern resulted in the closure of South PAG Channel and the corresponding development of Shell Key.

The heavily developed Long Key is located in Pinellas County in west-central Florida. The structured Blind Pass at the north end of the barrier island interrupts the southward longshore sediment transport, resulting in severe and chronic beach erosion along the northern portion of the island. Frequent beach nourishments were conducted to mitigate the erosion. In this study, the performance of the most recent beach nourishment in 2010 is quantified through time-series beach profile surveys. Over the 34-month period, the nourished northern portion of the island, Upham Beach, lost up to 330 m3/m of sand, with a landward shoreline retreat of up to 100 m. The middle portion of the island gained up to 25 m3/m of sand, benefiting from the sand lost from Upham Beach. The southern portion of Long Key lost a modest amount of sediment, largely due to Tropical Storm Debby, which approached from the south in June 2012. The severe erosion along Upham Beach is induced by a large negative longshore transport gradient. The beach here has no sand bar and retreated landward persistently over the 34-month study period. In contrast the profiles in the central section of the island generally have a sand bar which moved landward and seaward in response to seasonal and storm-induced wave-energy changes. The sand volume across the entire profile in the central portion of the island is mostly conserved. Two typical example beach profiles, LK3A and R157, were selected to examine the ability of the commonly used principal component analysis (PCA), also commonly known as empirical orthogonal function analysis (EOF), to identify beach profile ix changes induced by longshore and cross-shore sediment transport gradients. For the longshore-transport driven changes at the non-barred profile LK3A, the principal eigenvector accounted for over 91% of the total variance, with a dominant broad peak in the cross-shore distribution. At the barred R157, the profile changes were caused mainly by cross-shore transport gradients with modest contribution from longshore transport gradient; eigenvalue one only accounted for less than 51% of the total variance, and eigenvalues two and three still contributed considerably to the overall variance. In order to verify the uniqueness of the PCA results from LK3A and R157, five numerical experiments were conducted, simulating changes at a barred and non-barred beach driven by longshore, cross-shore, and combined sediment transport gradients. Results from LK3A and R157 compare well with simulated beach erosion (or accretion) due to variable longshore sediment transport gradients and due to both cross-shore and longshore sediment transport gradients, respectively. Different PCA results were obtained from different profile change patterns.