From 2008 to 2012, the total U.S. commercial landings of blue crabs (Callinectes sapidus Rathbun, 1896) averaged over 173 million lbs. Chesapeake Bay and its tributaries are important contributors to this fishery, providing greater than 30% of national commercial landings annually. In Chesapeake Bay, C. sapidus exhibits a complex life cycle in which mated females migrate to the saline waters of the Bay mouth to spawn. During migration, females can traverse multiple management jurisdictions, complicating effective management of this important fishery. Sustained declines in harvest have led to management strategies focused on protecting the female spawning stock in an attempt to enhance recruitment back into the Bay. This study presents the results of a broad scale mark-recapture study (n=7,072) in 11 Chesapeake Bay subestuaries and one coastal embayment, designed to track female migration and quantify spatial variation in exploitation rates of mature female blue crabs. Tagging was conducted in fall 2014 (September and October), when most females have matured and begin to migrate to the spawning grounds, and in summer 2015 (July), when additional females mature and migrate to the spawning grounds. Approximately 8.1% of tagged females were recaptured within one year of release. Overall, the exploitation rate of the 2015 blue crab spawning stock in Chesapeake Bay was 10.5%; however exploitation varied widely among systems (4.0-28.5%). This estimate is below both the management target and threshold exploitation rates and the population grew in subsequent years, suggesting recruitment overfishing of blue crabs was not occurring in Chesapeake Bay at this time.

If we want to understand how meroplankton utilize the water column and how their vertical distribution may influence horizontal advection, it is important to study their behavior in the various environments where they exist. In a well-mixed system with physical cues dampened, and no vertical layering, these organisms will have to depend on environmental cues such as light, tidal current, and tide cycle, as well as their own swimming ability to migrate vertically. Plankton and water samples were collected at three depths (near surface, midwater, near bottom) during the summers of 2013 and 2014 from sites within the main channel of the Intracoastal Waterway. Six taxonomic groups were collected including polychaetes, bivalves, gastropods, barnacles, tunicates, and crabs, and fell into one of three categories of vertical distribution. Certain preferences for vertical distribution, and habitat, of sessile invertebrates can increase, or provide refuge from, competition. To assess the potential competition for spatial resources between native and nonnative bivalves in the Guana Tolomato Matanzas estuary, settlement collectors with settlement plates at different depths were deployed for one month periods during the summers of 2013 and 2014 at two main channel sites and two feeder creek sites. Competition would likely be highest subtidally and within the main channel due to all species occurring in that habitat in higher numbers than the feeder creek.

Natural and local anthropogenic changes in estuaries (e.g., sea-level rise, navigation channel construction and loss of wetlands) interact with each other and produce non-linear effects. There is also a growing recognition that tides in estuaries are not stationary. These factors together are changing the estuarine water level regime, however the implications for extreme water levels remain largely unknown. Changes over the past century in many estuaries, such as channel deepening and streamlining for navigation have significantly altered the hydrodynamics of long waves, often resulting in amplified tides (a ~85% increase in Wilmington, NC since 1900) and storm surge in estuaries. This research focuses on establishing analytical and numerical models that simulate a wide range of systems and flow conditions that combine multiple flood sources: astronomical tide, storm surge, and high river flow. To investigate the effects of estuarine bathymetry conditions (e.g., channel depth, convergence length), hurricane conditions (e.g., pressure and wind field), river discharge, and surge characteristics (e.g., time scale and amplitude and relative phase) on tide and storm surge propagation, I develop an idealized analytical model and two numerical models using Delft-3D. The Cape Fear River Estuary, NC (CFRE), and St Johns River Estuary, FL (SJRE) are used as case studies to investigate flood dynamics. The analytical approach has been compared and verified with idealized numerical models. I use data recovery, data analysis, and idealized numerical modeling of the CFRE to investigate the effects of bathymetric changes (e.g., dredging and channel modification) on tidal and storm surge characteristics over the past 130 years. Data analysis and modeling results suggest that long-term changes in tides can be used along with the tidal analysis tools to investigate changes in storm surge. Analysis indicate that tidal range in Wilmington, NC (Rkm 47) has doubled to 1.55m since the 1880s, while a much smaller increase of 0.07m observed close to the ocean in Southport (Rkm 6) since the 1920s. Further, model results suggest that the majority of long term changes in tides of this system have been caused by deepening the system from 7m to 15.5m due to dredging, rather than by changes in the coastal tides. Numerical modeling using idealized, parametric tropical cyclones suggests that the amplitude of the worst-case, CAT-5 storm surge has increased by 40-60% since the nineteenth century. Storm surges are meteorologically forced shallow water waves with time scales that overlap those of the tidal bands. Using data, I show that the surge wave can be decomposed into two sinusoidal waves. Therefore, I analytically model surge via a 3-constituent analytical tide model, where the third constituent is the dominant semi-diurnal tide and friction is linearized via Chebyshev polynomials. A constant discharge is considered to approximate fluvial effects The analytical model is used to study how surge amplitude, surge time scale, and surge-tide relative phase affect the spatial pattern of amplitude growth and decay, and how depth changes caused by channel deepening influence the magnitude of a storm surge. I use non-dimensional numbers to investigate how channel depth, surge time scale and amplitude, surge asymmetry, and relative timing of surge to tides alter the damping or amplification of surge along the estuary. The non-dimensional numbers suggest that increasing depth has similar effects as decreasing the drag coefficient. Similarly, larger time scale has an equivalent effect on tide and surge as increasing depth due to channel deepening. Analytical model results show that the extent of the surge amplification is dependent on the geometry of the estuary (e.g., depth and convergence length) and characteristics of the surge wave. Both models show that much of the alterations of water levels in estuaries is due to channel deepening for navigation purposes and that the largest temporal change occur for surges with a high surge to D2 amplitude ratio and a short time scale. Model results farther indicate that surge amplitude decays more slowly (larger e-folding) in a deeper channel for all surge time scales (12hr-72hr). Another main finding is that, due to nonlinear friction, the location of maximum change in surge wave moves landward as the channel is deepened. Thus, changes in flood risk due to channel deepening are likely spatially variable even within a single estuary. Next, I use the verified analytical model and numerical models to investigate the effects of river flow on surge wave propagation, and spatial and temporal variability of compound flooding along an estuary. To model the historic SJRE, I digitize nautical charts of SJRE to develop a numerical model. Both the numerical and analytical models are used to investigate the contribution of tide, surge, and river flow to the peak water level for historic and modern system configurations. Numerical modeling results for hurricane Irma (2017) show that maximum flood water levels have shifted landward over time and changed the relative importance of the various contributing factors in the SJRE. Deepening the shipping channel from 5.5m to 15m has reduced the impacts of river flow on peak water level, but increased the effects of tide and surge. Sensitivity studies also show that peak water level decreases landward for all river flow scenarios as channel depth increases. Model results show that the timing of peak river flow relative to the time of maximum surge causes very large changes in the amplitude of total water level, and in river flow effects at upstream locations for modern configuration than for the historic model. Changes in surge amplitudes can be interpreted by the non-dimensional friction number, which shows that depth (h), surge time scale (T=1/w), and convergence length-scale (Le) affect the damping/amplification of both tides and surge waves. Overall, this study demonstrates that a system scale alteration in local storm surge dynamics over the past century is likely to have occurred in many systems and should be considered for system management. The results of this research give the scientists and engineer a better understanding of tide, river flow, and surge interactions, and thereby contribute to an understanding of how to predict storm surges and help mitigate their destructive impacts. Future system design studies also need to consider long-term and changes of construction and development activities on storm surge risk in a broader context than has historically been the case.

En la presente tesis se analizan los aspectos teóricos y prácticos necesarios para el desarrollo de un modelo numérico tridimensional válido para los estuarios típicos del Norte de España, cuyas características principales son la existencia de importantes gradientes de profundidad, , y de zonas que se inundan y se secan periódicamente debido al efecto de la marea astronómica.De la revisión del estado del conocimiento sobre modelado hidrodinámico tridimensional en zonas someras, se ha concluido que aunque existen varios modelos tridimensionales propuestos para estuarios, ninguno está preparado para su aplicación en los casos de estudio de esta tesis. La anterior aseveración está principalmente relacionada con tres temas fundamentales: sistema de coordenadas, representación de la turbulencia y simulación de la inundación - secado del dominio de cálculo. Se ha investigado con detalle estos aspectos y como resultado se ha desarrollado un modelo que incluye el resultado de la investigación realizada y que ha sido validado tanto con soluciones analíticas, como con datos de laboratorio y de campo.

Microphytobenthos (MPB) generally dominates total autotrophic biomass in temporarily open/closed estuaries (TOCEs) of South Africa. A comparative study of MPB biomass was undertaken in two KwaZulu-Natal TOCEs, the Mdloti and the Mhlanga. Both estuaries receive different volumes of treated sewage waters. The Mdloti receives 8 ML.d-1, while the Mhlanga receives 20 ML.d-1, resulting in a capping flow of 0.092 and 0.23 m3.s-1, respectively. Through these effluents, eutrophication is enhanced and periods of mouth opening are also increased and prolonged, particularly at the Mhlanga. The aim of this study was to investigate fluctuations in MPB biomass in the Mdloti and the Mhlanga systems, with emphasis on freshwater flow and the alternation of closed and open phases. Sediment samples for MPB biomass were collected on a monthly basis, between March 2002 and March 2003, in the lower (mouth), middle, and upper (head) reaches of the two estuaries. MPB biomass ranged from 1.33 to 391 mg chI a m-2 and from 1.7 to 313 mg chI a m-2 in the Mdloti and the Mhlanga, respectively. A I-way ANOVA revealed no significant differences in MPB chI a concentrations between the two estuaries for the entire data set (Fl, 76 =1.48, P > 0.05). At the Mdloti, MPB biomass varied considerably, with values ranging from 1.33 to 131 mg chI a m-2 during the open phase, and from 18 to 391 mg chI a m-2 during the closed phase. A Mann-Whitney U test confirmed the high significance of these differences between open and closed phases (U= 29, P < 0.001). At the Mhlanga, MPB biomass ranged from 7.0 to 313 mg chI a m-2 during the open phase, and from 1.7 to 267 mg chI a m-2 during the closed phase. Unlike what was observed at the Mdloti, the higher MPB values at the Mhlanga were not always associated with the closed mouth state. In relation to key physico-chemical and biological factors, grazing pressure exerted by the zooplankton community appeared to have played a major role in controlling MPB biomass. Zooplankton biomass was consistently and positively correlated to MPB biomass throughout the study period both at the Mdloti (r = 0040, P < 0.001) and at the Mhlanga (r = 0.33, p < 0.05). Unlike what was shown in previous studies, light attenuation was not significantly correlated with MPB biomass during the period ofthe study, either at the Mdloti or the Mhlanga. These results show that the opening and closing of the mouth play a key role on the MPB biomass of both estuaries. The Mdloti seems to function as a typical TOCE, with prolonged open and closed phases. The Mhlanga, on the other hand, lacks a prolonged closed phase. This, in turn, affects its entire trophic structure and functioning. / Thesis (M.Sc.)-University of KwaZulu- Natal, 2004.

Estuaries are dynamic features of a coastline whose sediments are influenced by riverine and marine processes. Periodic events such as floods, as well as variations in mouth status, greatly affect the energy levels within an estuary and subsequently the amount of sediment erosion and deposition that takes place. Concurrently, pollutants are transported and deposited into estuaries and can reside in the sediments for many years. The estuaries of the eThekwini Municipality in KwaZulu-Natal, South Africa, are exposed to a variety of pollutants; however with the expanding industrial sector within this region, metal contamination is of concern. This study investigates the sedimentology and geochemical variations of six estuaries within the municipality namely, the uTongati, uMdloti, uMgeni, Isipingo and uMbokodweni estuaries as well as the Durban Harbour. To determine the spatial variations in estuarine sedimentology, sediment cores were collected longitudinal to the estuary axis. The core samples were analysed for sediment colour, texture and organic matter content. To assess the geochemical variations, core samples were analysed for Zn, Cu, Cr, Ni, Pb, As, Fe, Al, Ca, S, P, Mg, Mn, Cd and V concentrations. Some samples were also carbon dated to provide a temporal aspect to the sediment and geochemical variations. Descriptive and graphic techniques were used to examine the sedimentology within the estuaries; and the geochemical data was analysed with the use of multivariate statistics. Additionally, pollution indices and sediment quality guidelines were utilized to assess the pollution levels within the sediments. The results indicated that lower energy environments caused by protracted mouth closures in the uMdloti and Isipingo estuaries accounted for large amassing of fines. In contrast, the accumulation of mixed coarse and fine sediments in the uTongati and uMgeni estuaries was an indication of high fluvial flows and open mouth conditions. All carbon dated ages for all estuaries were greater than 700 years which may be attributed to a combination of scouring effects from past and recent flood events and also possibly due to the deposition of re-worked older sediments from upstream. Low metal concentrations were found within the sediments of all estuaries, and the presence of fines and organic matter governed their concentration variations with depth. The uMgeni and uMbokodweni estuaries which are located immediately downstream of industrial and urban areas, were found to contain relatively higher concentrations of elements Pb, Cu, As and Ni. These metals showed high enrichment within the sediments; however actual concentrations were below sediment quality guideline levels. General pollution levels within all estuaries were very low, and can be attributed to the climatic influences within this region which has a ‘cleansing’ effect on the estuarine environments in removing contaminants. / Thesis (M.Sc.)-University of KwaZulu-Natal, Durban, 2014.

The St Lucia estuarine system, Africa’s largest estuarine lake, is characterised by cyclic changes from hypersaline to oligo/mesohaline conditions in response to alternations between drought and wetter than average years. In addition, St Lucia also experiences stochastic disturbances, such as flooding events that rapidly decrease salinity levels. Due to their sessile and slow moving nature, bivalves are particularly vulnerable to rapid or prolonged changes in the physico-chemical environment. The recent freshwater deprivation crisis that prevailed for the last decade resulted in a significant loss in bivalve species richness within the system. An annotated and illustrated bivalve census revealed the occurrence of twenty-four species within St Lucia between the years 1925 and 2011. However, only six species were recorded during the most recent survey in March 2011. The infaunal razor clam, Solen cylindraceus, and the epifaunal brackwater mussel, Brachidontes virgiliae, are currently the dominant bivalve species within St Lucia. This study, therefore, aimed to record the species richness of bivalves found in Lake St Lucia and to investigate key biological aspects of the two dominant bivalve taxa within the system, under different salinity regimes. Experiments revealed that S. cylindraceus can tolerate salinities between 15 and 65, while B. virgiliae prefers salinity levels ranging from freshwater to 20. The varying tolerance limits, therefore, dictate the distribution of these species during different climatic conditions within the estuarine lake. During wet periods, S. cylindraceus is restricted to the northern reaches, unable to tolerate the oligohaline conditions present in the rest of the system. Conversely, B. virgiliae, often restricted to the Narrows, becomes ubiquitous throughout the system under such conditions. Solen cylindraceus can reach a maximum length of 95 mm. However, in the St Lucia estuarine system, specimens seldom exceed a length of 55 mm, probably because prevailing/re-occurring harsh conditions prevent them from reaching maximum size. In situ measurements of this species also revealed less growth during the first year of life than for the same species in different systems. While B. virgiliae is substantially smaller than S. cylindraceus, the high densities that this species is able to attain makes it an important grazer with the potential to have significant feeding impacts on the local phytoplankton biomass. Results showed that in localised areas, B. virgiliae populations may consume up to eight times the available phytoplankton biomass. These key bivalve species are strongly influenced by the fluctuation in climatic conditions from wet to dry phases. Thus, understanding the effects that climatic shifts have on key estuarine species is essential, as flood and drought events are predicted to increase in frequency, intensity and duration as a result of global climate change. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2014.

The St Lucia estuarine lake system in South Africa is part of a UN- ESCO World Heritage site and a Ramsar wetland of international importance. Like many estuarine systems worldwide St Lucia has experienced signi cant anthropogenic impacts over the past century including catchment land use changes, water diversions/abstractions and inlet manipulation. In addition, the system has recently su ered losses in species diversity and abundance following unprecedented hy- persaline conditions and desiccation. Questions regarding its sustain- ability have motivated a reevaluation of management decisions made in the past and of options for the future. To understand the func- tioning of the system, it is necessary to analyse it holistically in terms of the physical processes and their interaction with the biology. This study focusses on aspects of the biophysical interactions in the estu- arine complex, and aims to provide new knowledge to underpin the development of improved models for predicting the response of the system to anthropogenic interventions. A model for the water and salt budgets was used to investigate what if scenarios in terms of past anthropogenic interventions, in particular the e ects of diverting the Mfolozi River from St Lucia. Furthermore, the risks of hypersalinity and desiccation were assessed for each sce- nario. Integrating these modeled scenarios with observed biological responses to physicochemical changes suggested that large long-term changes in the ecological structure can be expected in the di erent management scenarios. To validate this, the ecosystem response to changing environmental responses was quantitatively assessed using ecological network analysis. Long-term simulations show that the separation of the Mfolozi and St Lucia mouths had a signi cant impact on the functioning of the St Lucia system. The Mfolozi plays a pivotal role in maintaining a more stable mouth state regime and provides a vital source of freshwater during dry conditions. The con guration of the Mfolozi/St Lucia inlet plays a key role in the physico-chemical environment of the system and in uences the system's susceptibility to desiccation and hypersaline conditions. Ecosystem indices revealed that the water level, salinity and mouth state have a signi cant impact on species abundance and diversity as well as the ecological structure and functioning of the system. In addition, ecosystem indices show that the system recovers rapidly during favourable conditions. The arti cial separation of the St Lucia and Mfolozi inlets underpins the most signi cant impacts on the water and salt budget of the lake and its reversal is key to the sustainability of the system. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2013.

Thesis (M.S.)--Florida State University, 2005. / Advisor: Dr. Robert Deyle, Florida State University, College of Social Sciences, Dept. of Urban and Regional Planning. Title and description from dissertation home page (viewed June 13, 2005). Document formatted into pages; contains ix, 70 pages. Includes bibliographical references.

Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / Esta tese tem por objetivo propor uma estratégia de obtenção automática de parâmetros hidrodinâmicos e de transporte através da solução de problemas inversos. A obtenção dos parâmetros de um modelo físico representa um dos principais problemas em sua calibração, e isso se deve em grande parte à dificuldade na medição em campo desses parâmetros. Em particular na modelagem de rios e estuários, a altura da rugosidade e o coeficiente de difusão turbulenta representam dois dos parâmetros com maior dificuldade de medição. Nesta tese é apresentada uma técnica automatizada de estimação desses parâmetros através deum problema inverso aplicado a um modelo do estuário do rio Macaé, localizado no norte do Rio de Janeiro. Para este estudo foi utilizada a plataforma MOHID, desenvolvida na Universidade Técnica de Lisboa, e que tem tido ampla aplicação na simulação de corpos hídricos. Foi realizada uma análise de sensibilidade das respostas do modelo com relação aos parâmetros de interesse. Verificou-se que a salinidade é uma variável sensível a ambos parâmetros. O problema inverso foi então resolvido utilizando vários métodos de otimização através do acoplamento da plataforma MOHID a códigos de otimização implementados em Fortran. O acoplamento foi realizado de forma a não alterar o código fonte do MOHID, possibilitando a utilização da ferramenta computacional aqui desenvolvida em qualquer versão dessa plataforma, bem como a sua alteração para o uso com outros simuladores. Os testes realizados confirmam a eficiência da técnica e apontam as melhores abordagens para uma rápida e precisa estimação dos parâmetros. / This thesis presents a strategy for automatically obtaining hydrodynamic and transport parameters by means of the solution of inverse problems. Obtaining the parameters of a physical model represents a major problem in its calibration, and this is largely due to the difficulty associated to the field measurements of these parameters. In particular by modeling rivers and estuaries, the roughness height and the turbulent diffusion coefficient represent two of the most difficult parameters to measure or estimate. Here, an automated technique for estimation of these parameters through an inverse problem is applied to a model of the Macaé estuary, located in northern Rio de Janeiro. For this investigation, hydrodynamic and transport models were built in the MOHID platform, developed in the Technical University of Lisbon, which has had wide application in simulation of water bodies. A sensitivity analysis was performed regarding the model responses with respect to the parameters of interest. It was verified that salinity is a sensitive variable for both parameters. The inverse problem was then solved using various optimization methods by coupling the MOHID platform to optimization codes implemented in Fortran. The coupling was carried in a way to not change the MOHID source code, allowing the use of the computational tool here developed in any version of this platform, as well as its modification for use with other simulators. The tests confirm the efficiency of the technique and suggest the best approaches for a fast and accurate estimation of the parameters.