Using a composite grid approach in a complex coastal domain to estimate estuarine residence time

This paper is not subject to U.S. copyright. The definitive version was published in Computers & Geosciences 36 (2010): 921-935, doi:10.1016/j.cageo.2009.11.008.We investigate the processes that influence residence time in a partially mixed estuary using a three-dimensional circulation model. The complex geometry of the study region is not optimal for a structured grid model and so we developed a new method of grid connectivity. This involves a novel approach that allows an unlimited number of individual grids to be combined in an efficient manner to produce a composite grid. We then implemented this new method into the numerical Regional Ocean Modeling System (ROMS) and developed a composite grid of the Hudson River estuary region to investigate the residence time of a passive tracer. Results show that the residence time is a strong function of the time of release (spring vs. neap tide), the along-channel location, and the initial vertical placement. During neap tides there is a maximum in residence time near the bottom of the estuary at the mid-salt intrusion length. During spring tides the residence time is primarily a function of along-channel location and does not exhibit a strong vertical variability. This model study of residence time illustrates the utility of the grid connectivity method for circulation and dispersion studies in regions of complex geometry.W.R. Geyer was supported by the Hudson River Foundation Grant 002/07A,H.G.Arango by the Office of Naval Research,and John Warner was supported by the USGS Community Sediment Modeling Project

Role of Baroclinic Processes on Flushing Characteristics in a Highly Stratified Estuarine System, Mobile Bay, Alabama

Flushing of an estuary quantifies the overall water exchange between the estuary and coastal ocean and is crucially important for water quality as well as biological and geochemical processes within the system. Flushing times and freshwater age in Mobile Bay were numerically calculated under realistic and various controlled forcing conditions. Their responses to external forcing were explained by the three‐dimensional characteristics of general circulation in the system. The flushing time ranges from 10 to 33 days under the 25th–75th percentile river discharges, nearly half of the previous estimates based on barotropic processes only, suggesting the important contribution of baroclinic processes. Their influence, quantified as the “new ocean influx,” is on the same order of the river discharge under low to moderate river discharge conditions. The baroclinic influence increases and then decreases with increasing river discharge, aligning with the response of horizontal density gradient. By enhancing the net influx from the ocean mainly through density‐driven circulation, baroclinic processes contribute to reduce flushing times. The three‐dimensional circulation, which differs greatly between the wet and dry seasons, explains the temporal and spatial variations of the flushing characteristics. Wind forcing influences the three‐dimensional circulation in the system with easterly and northerly winds tending to reduce the flushing time, while southerly and westerly winds the opposite

Sediment transport due to extreme events : the Hudson River estuary after tropical storms Irene and Lee

Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 40 (2013): 5451–5455, doi:10.1002/2013GL057906.Tropical Storms Irene and Lee in 2011 produced intense precipitation and flooding in the U.S. Northeast, including the Hudson River watershed. Sediment input to the Hudson River was approximately 2.7 megaton, about 5 times the long-term annual average. Rather than the common assumption that sediment is predominantly trapped in the estuary, observations and model results indicate that approximately two thirds of the new sediment remained trapped in the tidal freshwater river more than 1 month after the storms and only about one fifth of the new sediment reached the saline estuary. High sediment concentrations were observed in the estuary, but the model results suggest that this was predominantly due to remobilization of bed sediment. Spatially localized deposits of new and remobilized sediment were consistent with longer term depositional records. The results indicate that tidal rivers can intercept (at least temporarily) delivery of terrigenous sediment to the marine environment during major flow events.This research was supported by grants from the Hudson Research Foundation (002/07A) and the National Science Foundation (1232928).2014-04-1

Using tracer variance decay to quantify variability of salinity mixing in the Hudson River Estuary

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Warner, J. C., Geyer, W. R., Ralston, D. K., & Kalra, T. Using tracer variance decay to quantify variability of salinity mixing in the Hudson River Estuary. Journal of Geophysical Research: Oceans, 125(12), (2020): e2020JC016096, https://doi.org/10.1029/2020JC016096.The salinity structure in an estuary is controlled by time‐dependent mixing processes. However, the locations and temporal variability of where significant mixing occurs is not well‐understood. Here we utilize a tracer variance approach to demonstrate the spatial and temporal structure of salinity mixing in the Hudson River Estuary. We run a 4‐month hydrodynamic simulation of the tides, currents, and salinity that captures the spring‐neap tidal variability as well as wind‐driven and freshwater flow events. On a spring‐neap time scale, salinity variance dissipation (mixing) occurs predominantly during the transition from neap to spring tides. On a tidal time scale, 60% of the salinity variance dissipation occurs during ebb tides and 40% during flood tides. Spatially, mixing during ebbs occurs primarily where lateral bottom salinity fronts intersect the bed at the transition from the main channel to adjacent shoals. During ebbs, these lateral fronts form seaward of constrictions located at multiple locations along the estuary. During floods, mixing is generated by a shear layer elevated in the water column at the top of the mixed bottom boundary layer, where variations in the along channel density gradients locally enhance the baroclinic pressure gradient leading to stronger vertical shear and more mixing. For both ebb and flood, the mixing occurs at the location of overlap of strong vertical stratification and eddy diffusivity, not at the maximum of either of those quantities. This understanding lends a new insight to the spatial and time dependence of the estuarine salinity structure.This study was funded through the Coastal Model Applications and Field Measurements Project and the Cross‐shore and Inlets Project, US Geological Survey Coastal Marine Hazards and Resources Program. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US Government

Tracer and Timescale Methods for Passive and Reactive Transport in Fluid Flows

Geophysical, environmental, and urban fluid flows (i.e., flows developing in oceans, seas, estuaries, rivers, aquifers, reservoirs, etc.) exhibit a wide range of reactive and transport processes. Therefore, identifying key phenomena, understanding their relative importance, and establishing causal relationships between them is no trivial task. Analysis of primitive variables (e.g., velocity components, pressure, temperature, concentration) is not always conducive to the most fruitful interpretations. Examining auxiliary variables introduced for diagnostic purposes is an option worth considering. In this respect, tracer and timescale methods are proving to be very effective. Such methods can help address questions such as, "where does a fluid-born dissolved or particulate substance come from and where will it go?" or, "how fast are the transport and reaction phenomena controlling the appearance and disappearance such substances?" These issues have been dealt with since the 19th century, essentially by means of ad hoc approaches. However, over the past three decades, methods resting on solid theoretical foundations have been developed, which permit the evaluation of tracer concentrations and diagnostic timescales (age, residence/exposure time, etc.) across space and time and using numerical models and field data. This book comprises research and review articles, introducing state-of-the-art diagnostic theories and their applications to domains ranging from shallow human-made reservoirs to lakes, river networks, marine domains, and subsurface flow

Exploring the Influence of Diurnal Forcing on Tidal Inlet Exchange and the Impact on the movement of Oxygen Depleted Waters in the Mississippi Sound and Bight Region

A small yet notable hypoxic event manifests east of the Birdfoot Delta in the Mississippi Sound and Bight (MSAB). The shallow shelf environment of the MSAB is affected by a host of complex physical interactions and separating the influences of each process is difficult to accomplish with in-situ data alone. A physical model using high-resolution atmospheric forcing has been developed which provides insights into the physical interactions in this coastal marine system heavily influenced by freshwater plumes and diurnal wind forcing. Twin experiments using a high temporal (hourly) and spatial (0.01 deg) resolution meteorological analysis product, along with a temporally filtered version, have been performed to investigate the influence of the diurnal sea breeze on the flushing of estuarine waters onto the shelf. Results from these numerical experiments have provided a detailed perspective on flushing times and the impacts on the appearance of the poorly understood hypoxic event in the MSAB. The higher resolution atmospheric forcing has demonstrable impacts on the hydrodynamics of the MSAB. The twin experiments highlight the influence of diurnal sea-breeze forcing, which impacts bottom water flushing times in areas known to be hypoxia hotspots. The experiments show that the probability of hypoxia formation decreases when diurnal energy is present due to its impact on water column stability. Finally, the wind fields used to conduct the twin experiments are combined to create a seasonal evolution of the sea-land breeze circulation within the MSAB that was not previously realized using the in-situ data alone

Total exchange flow, entrainment, and diffusive salt flux in estuaries

Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 1205-1220, doi:10.1175/JPO-D-16-0258.1.The linkage among total exchange flow, entrainment, and diffusive salt flux in estuaries is derived analytically using salinity coordinates, revealing the simple but important relationship between total exchange flow and mixing. Mixing is defined and quantified in this paper as the dissipation of salinity variance. The method uses the conservation of volume and salt to quantify and distinguish the diahaline transport of volume (i.e., entrainment) and diahaline diffusive salt flux. A numerical model of the Hudson estuary is used as an example of the application of the method in a realistic estuary with a persistent but temporally variable exchange flow. A notable finding of this analysis is that the total exchange flow and diahaline salt flux are out of phase with respect to the spring–neap cycle. Total exchange flow reaches its maximum near minimum neap tide, but diahaline salt transport reaches its maximum during the maximum spring tide. This phase shift explains the strong temporal variation of stratification and estuarine salt content through the spring–neap cycle. In addition to quantifying temporal variation, the method reveals the spatial variation of total exchange flow, entrainment, and diffusive salt flux through the estuary. For instance, the analysis of the Hudson estuary indicates that diffusive salt flux is intensified in the wider cross sections. The method also provides a simple means of quantifying numerical mixing in ocean models because it provides an estimate of the total dissipation of salinity variance, which is the sum of mixing due to the turbulence closure and numerical mixing.T. Wang was supported by the Open Research Fund of State Key Laboratory of Estuarine and Coastal Research (Grant SKLEC-KF201509), the Fundamental Research Funds for the Central Universities (Grant 2017B03514), and the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant XDA11010203). W. R. Geyer was supported by NSF Grant OCE 0926427 and ONR Grant N00014-16-1-2948. P. MacCready was supported by NSF Grant OCE-1634148.2017-09-1

Sediment transport time scales and trapping efficiency in a tidal river

Author Posting. © American Geophysical Union, 2017. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Earth Surface 122 (2017): 2042–2063, doi:10.1002/2017JF004337.Observations and a numerical model are used to characterize sediment transport in the tidal Hudson River. A sediment budget over 11 years including major discharge events indicates the tidal fresh region traps about 40% of the sediment input from the watershed. Sediment input scales with the river discharge cubed, while seaward transport in the tidal river scales linearly, so the tidal river accumulates sediment during the highest discharge events. Sediment pulses associated with discharge events dissipate moving seaward and lag the advection speed of the river by a factor of 1.5 to 3. Idealized model simulations with a range of discharge and settling velocity were used to evaluate the trapping efficiency, transport rate, and mean age of sediment input from the watershed. The seaward transport of suspended sediment scales linearly with discharge but lags the river velocity by a factor that is linear with settling velocity. The lag factor is 30–40 times the settling velocity (mm s−1), so transport speeds vary by orders of magnitude from clay (0.01 mm s−1) to coarse silt (1 mm s−1). Deposition along the tidal river depends strongly on settling velocity, and a simple advection-reaction equation represents the loss due to settling on depositional shoals. The long-term discharge record is used to represent statistically the distribution of transport times, and time scales for settling velocities of 0.1 mm s−1 and 1 mm s−1 range from several months to several years for transport through the tidal river and several years to several decades through the estuary.Hudson River Foundation Grant Number: 004/13A; National Science Foundation Grant Number: 13251362018-05-0

Modelação de pradarias marinhas intertidais numa laguna costeira mesotidal

Seagrass meadows are important habitats of marine plants, adapted to the colonization of coastal and estuarine environments, which provide important functions within the ecosystem. The remarkable decline of seagrass meadows at regional/local (Ria de Aveiro) and global scales has presented however negative implications for the sustainability of the ecosystems where they follow this trend. In this context, the main objective of this work was to improve the present knowledge about seagrass dynamics in the Ria de Aveiro, from a multidisciplinary viewpoint (experimental data collection and treatment and numerical modelling), as well as to anticipate potential changes at the system level in these communities. Therefore, it is intended to contribute to the promotion of adequate management and conservation strategies to minimize its decline and enhance its recovery. From the application of a conceptual DSPIR framework (Drivers-Pressures-State-Impacts- Responses), the results pointed that gradual changes in hydrodynamic characteristics are the basis of the local decline of these communities, presently colonized by monospecific intertidal meadows of Zostera noltei. The scarce availability of seagrass models is even more prominent when dealing with intertidal communities, subject to alternating periods of exposure to air and submergence. As so, the inherent peculiarities of intertidal seagrass Z. noltei communities were investigated, showing a greater influence of the sedimentary characteristics on the relative water content of the plant, rather than the air exposure time. Afterwards, it was developed a seagrass biological model together with a desiccation model of the plant, in order to suppress the previously identified gap, both of which were later coupled to the water quality model (Delft3D-WAQ). The numerical model was calibrated using experimental data collected in the study area (Mira Channel), showing a reliable reproduction of the state variables described by means of above and belowground biomass. However, the present set up needs to be improved, namely in what regards sedimentplant interface and internal nutrient dynamics, before it can be applied to other systems with similar challenges. The performance of the numerical model was analysed through different methodologies that presented divergent results, which suggests the application of further approaches for a robust conclusion. A sensitivity analysis was computed, showing that the parameters used to describe the dependence of the ambient temperature (water and air) are the most sensitive, suggesting that these should be particularly addressed in future experimental surveys, by increasing the frequency of the in situ measurements. Two exploratory simulations of extreme event, extreme river flow and heat-wave, respectively showed a decrease in the favourable conditions for seagrass presence, according to the water velocity and salinity; and clear negative impacts on seagrass growth. Following a prospective viewpoint, different evolutionary scenarios to the future, resulting from the foreseen climate change, were set according to the more and less pessimistic projection (RCP 4.5 and RCP 8.5). The numerical model projections pointed out for a noticeable loss of colonised areas by seagrass (between around 30 and 70%, respectively) compared to the present situation. The multiple stressors analysed generally showed a synergistic effect on the loss of the relative area of seagrass, compared to the isolated sum of each of the factors, which highlights the complex and intrinsic relations established between them. The areas colonized by seagrass meadows that showed greater resilience, to the two simulated climate change scenarios, are located in the south and northwest areas of the central lagoon. The spatial distribution of the anomalies between the reference and the climate change scenarios, showed no uniform pattern of variation, occurring areas with descreased favourable conditions for seagrass presence, but also some areas that verified an improvement of these conditions. For a more effective and holistic approach to the natural evolution and modelling of these systems, a wider spatial and temporal coverage of biotic and abiotic descriptors of these communities should be performed. Moreover, the overview of the ongoing and forthcoming anthropogenic actions must also be included, in the context of the socio-economic development of the region, as well as the framework of the future scenarios in the scope of climate change (temporal scale referred to the end of the century). As so, the management actions can be implemented to promote the resilience of these habitats and assure the services provided by the ecosystem.As pradarias marinhas constituem importantes habitats de plantas superiores, adaptadas à colonização de ambientes costeiros e estuarinos, que desempenham importantes funções nestes ecossistemas. O seu declínio acentuado verificado a escalas regionais/locais (Ria de Aveiro) e globais tem, no entanto, apresentado implicações nefastas para a sustentabilidade dos ecossistemas onde estão inseridas. Neste contexto, o objectivo principal deste trabalho consistiu em aprofundar o conhecimento presente da dinâmica das pradarias marinhas na Ria de Aveiro, sob o ponto de vista multidisciplinar (colheita e tratamento de dados experimentais e modelação numérica), bem como prever as potenciais alterações ao nível do sistema nestas comunidades. Desta forma, pretende-se contribuir para a promoção de estratégias de conservação adequadas para minimizar o seu declínio e potenciar a sua recuperação. Partindo da aplicação de um modelo conceptual DPSIR (Drivers-Pressures- State-Impacts-Responses), concluiu-se que as alterações graduais nas características hidrodinâmicas estão na base do declínio local destas comunidades, presentemente colonizadas por pradarias monoespecíficas intertidais de Zostera noltei. A escassez de modelos numéricos de pradaria é acentuada, sendo ainda mais proeminente quando se tratam de comunidades intertidais, sujeitas a períodos alternados de exposição ao ar e submersão. Desta forma, as particularidades inerentes às comunidades de pradarias intertidais foram investigadas, mostrando maior influência das características sedimentares no teor relativo de água da planta, em detrimento do tempo de exposição ao ar. Posteriormente, foi desenvolvido um modelo biológico de pradaria, juntamente com um modelo de dessecação da planta, com vista a suprimir a lacuna previamente identificada, sendo ambos posteriormente acoplados ao modelo de qualidade da água (Delft3D-WAQ). Utilizando os dados experimentais colhidos na área de estudo (Canal de Mira) calibrou-se o modelo numérico, tendo-se verificado uma reprodução fiável das variáveis-estado descritas pela biomassa aérea e subterrânea. Porém, a presente configuração requer melhorias adicionais, nomeadamente no que respeita à interface sedimento-planta e dinâmica interna de nutrientes, previamente a ser passível de ser aplicado a outros sistemas com desafios semelhantes. O desempenho do modelo numérico foi analisado por diferentes metodologias que apresentaram resultados divergentes, o que sugere a necessidade de desenvolvimento e aplicação de metodologias adicionais para uma conclusão robusta. Foi realizada uma análise de sensibilidade, que permitiu aferir que os parâmetros usados para descrever a dependência da temperatura ambiente (água e ar) são os mais sensíveis. Deste modo, salienta-se a sua potencial importância e sugere-se a sua consideração em planeamentos experimentais futuros com maior frequência de amostragem nas medições in situ. Numa abordagem exploratória, simularam-se dois eventos extremos, caudal fluvial extremo e onda de calor, tendo os resultados apresentado, respectivamente, uma diminuição das condições favoráveis para a presença de pradarias em termos de velocidade da corrente e salinidade, e um claro decréscimo no crescimento da planta. Seguindo uma abordagem prospectiva, estabeleceram-se diferentes cenários evolutivos para o futuro, resultantes das expectáveis alterações climáticas, de acordo com a projecção mais e menos pessimista (RCP 4.5 e RCP 8.5). As previsões numéricas obtidas indicam uma perda acentuada de áreas colonizadas por pradarias marinhas (entre aproximadamente 30 e 70%, respectivamente) comparativamente à situação presente. As áreas colonizadas por pradarias que mostraram uma maior resiliência, nos dois cenários de alterações climáticas, situam-se na zona sul e noroeste da laguna central. Na análise espacial da anomalia entre o cenário de referência e de alterações climáticas, não se verificou um padrão uniforme, havendo áreas que apresentam um decréscimo nas condições favoráveis para a presença de pradarias marinhas, simultaneamente à ocorrência de áreas que apontam para um melhoramento das mesmas condições. Para uma abordagem mais efectiva e holística da evolução natural e modelação destes sistemas, deve considerar-se uma maior cobertura espacial e temporal dos descritores bióticos e abióticos destas comunidades. Deve ser ainda incluído o levantamento das actividades antropogénicas decorrentes e previstas no contexto do desenvolvimento socio-económico da região (escala temporal até meio do século), e ainda, deve ser feito o enquadramento nos cenários futuros no contexto das alterações climáticas (escala temporal até final do século), para que medidas de gestão possam ser implementadas no sentido de promover a resiliência destes habitats, de forma a garantir os serviços prestados.Projecto LAGOONS – FP7/2007-2013; Projecto AquiMap (MAR-02.01.01-FEAMP-0022)Programa Doutoral em Biologi