The Port of Gulfport along with others on the Mississippi Gulf Coast experience large amounts of sediment deposition within their harbors and channels. The primary tool for sediment removal is dredging, which can be expensive and create downtimes in port operations. Research will study deposited material to determine its sources and suggest solutions for reduction of sediment deposition using structures, technologies and/or practices. Instruments used for such studies will be clam-shell dredges, Niskin tubes, and automatic samplers to test bed sediment gradation, suspended point sediments and tidal variations in suspended sediments, respectively. Additionally, fluid mud data will be retrieved from the U.S. Army Corps of Engineers ERDC. This combination of data will assist in the development of solutions for reducing sediment deposition within the port. Furthermore, research will be performed to compare the estimated throughput without dredging to throughput with dredging. This estimation will be shown in a simulated model.

The purpose of this work is to generate a shore profile algorithm to be used in estuaries dominated by fine sediments. Numerical models are continually evolving to enhance the overall accuracy of results. However, the typical shore profile is defined as a vertical wall. This work defines the shore as a nonlinear profile which will provide more realistic models. A variety of shore profile equations were examined and tested against a field site, Weeks Bay, Alabama. The most applicable, an equation by S. C. Lee, was modified in order to calculate the entire shore profile length. The distance from the land-water interface to the depth at which sedimentation is negligible can now be modeled with a single equation. Recommendations for the practical aspect of implementation into a numerical model are also considered.

Previous research efforts have shown that fish and macroinvertebrates are responsive to fine sediment in streambeds. Excess fine sediment (<2mm in diameter) impairs over 40,000 miles of streams in the U.S., degrading habitat quality for many aquatic species. Embeddedness (emb, %), a measure of fine sediment in gravel bed streams, is negatively correlated with bankfull shear velocity (u*, m/s). This relationship can be modeled by emb = au*b, with baseline coefficient values of a = 10 and b = –1. The purpose of this thesis was to investigate the applicability of this relationship across the U.S., to begin to quantify the variation of embeddedness in time, and to determine the applicability of embeddedness as a habitat metric for lotic biota. The areas that were studied included Stroubles Creek at the Virginia Tech Stream Lab, the Upper Roanoke River Basin in southwest Virginia, and Level II and III ecoregions nationwide with the U.S. EPA National Rivers and Streams Assessment dataset. Nationally, measurements of embeddedness were higher than modeled in areas with higher sediment supply, and lower than modeled in regions with low fine sediment supply. By calculating shear velocity through remotely sensed channel geometry metrics, embeddedness may be predicted throughout a stream network. Various biotic metrics were found to be correlated to embeddedness, with regional variation. Burrowing macroinvertebrate taxa, which may use increased sand to escape predation, increased with increasing embeddedness while the number of Ephemeroptera, Plecoptera, Trichoptera (EPT) taxa, the number of lithophilic spawning fish, and the number of salmonid taxa decreased with increasing embeddedness. Highly embedded substrate is generally considered poor habitat, which was supported by a trend of decreasing intolerant fish taxa with increasing embeddedness. Richness (total number of taxa) did not show a significant correlation, indicating that embeddedness, and fine sediment in general, is not necessarily an impairment to all stream habitat, but is impactful for particular taxa. / Master of Science / Previous research has shown that fish and macroinvertebrates are responsive to fine sediment in streambeds. Excess fine sediment (sand, silt, and clay) impairs over 40,000 miles of streams in the U.S., degrading habitat quality for many aquatic species. Embeddedness (emb, %), a measure of fine sediment in gravel bed streams, decreases with increasing bankfull shear velocity (u*, m/s), a measure of a stream's ability to move a particular size of sediment. The purpose of this thesis was to investigate the relationship between embeddedness and shear velocity in varying areas, to begin to quantify the variation of embeddedness in time, and to determine the applicability of embeddedness as a habitat metric for stream biota. The areas that were studied included Stroubles Creek at the Virginia Tech Stream Lab, the Upper Roanoke River Basin in southwest Virginia, and Level II and III ecoregions nationwide with the U.S. EPA National Rivers and Streams Assessment dataset. Nationally, measurements of embeddedness were higher in areas that may have higher sediment supply, and lower in regions with low fine sediment supply. By calculating shear velocity with remotely available stream data, embeddedness may be predicted throughout a stream network and compared with biota in those locations. Various biotic metrics were found to be correlated to embeddedness, with regional variation. Burrowing macroinvertebrate taxa, which may use increased sand to escape predation, increased with increasing embeddedness while the number of Ephemeroptera, Plecoptera, Trichoptera (EPT) taxa, the number of lithophilic spawning fish, and the number of salmonid taxa decreased. Highly embedded substrate is generally considered poor habitat, which was supported by a trend of decreasing intolerant fish taxa with increasing embeddedness.

Detailed information about negative effects of fine sediments on early life stages of brook trout (Salvelinus fontinalis) in southern Appalachian streams is lacking. Information on survival to different stages of egg and alevin development could indicate critical timing of sediment impacts. This study was designed to determine the effects of fine sediments (0.43-0.85 rom in diameter) on survival of brook trout eggs through early development stages under controlled laboratory and field conditions. Recently fertilized eggs were loaded into Whitlock-Vibert (W-V) boxes lined with 0.4 rom Nitex netting that contained mixtures of gravel and fine sediments. Survival to eyed, hatched, and emerged stages of development was determined for six amounts of fine sediment (0-25% by weight) in the laboratory study and for three amounts of fine sediment (0-20% by weight) in the field study. Survival in laboratory systems to each stage of development was inversely related to the percentage of fine sediment; even at low levels of fine sediment survival was reduced. In the field study, fine sediment may have played a role in the survival success of developing embryos, but determining a definitive relationship was confounded by effects of scouring flows and fungal infestations. The fungus Saprolegnia spp., may have increased the mortality rate of viable eggs and facilitated the disintegration of nonviable embryos, especially in the field study. Brook trout are sensitive to increasing levels of fine sediment through early development. However under field conditions such an effect may be difficult detect. / Master of Science

Fine-grained sediment accumulation in the interstices of gravel beds is a key factor in degrading riverine habitats. However, interstitial deposits are highly dynamic and are not sufficiently understood. This work enhances the understanding of interstitial fine sediment deposition by investigating interstitial storage and ingress, flow, suspended sediment and gravel bed character. Furthermore, this work introduces a numerical suspended sediment deposition model with the power to predict patterns of interstitial ingress. The investigation of interstitial deposition were carried out on two levels. Both data orginating from flume experiments and from three locations of the River Culm, Devon, UK was collected. The experimental data showed the significant influence of small scale variations in flow and bed character and their influence on interstitial ingress. The field investigation showed clear differences in interstitial fine-grained sediment for the different river reaches and an overall higher interstitial ingress compared to recent published data. The numerical model development was realised in a two-step approach. First, the model was coded and calibrated for the flume scale processes and, second, an upscaled reach scale model was devolped for the field data. This reach scale suspended sediment deposition model included flow information, for which depthaveraged two dimensional hydrodynamic models were developed with the software Delft3D. The overall explanatory power of the model at this state is not satisfactory with regards to local deposition distribution. A separate chapter discusses the possible causes and implications of this short coming for further research from a data aquisition and modelling perspective.

Thesis advisor: Gail Kineke / The Penobscot River Estuary is heavily contaminated with mercury; previous studies indicate maximum mercury concentrations of 4.6 ppm within the Frankfort Flats reach. The transport and trapping of this contaminant is linked to the transport and trapping of fine sediment within the estuary. Hydrographic and flow measurements, coupled with a spatial and temporal characterization of the bottom sediments, were performed during and following the freshet in 2010 to determine the mechanisms driving sediment transport and trapping within the estuary. The Penobscot River likely has a turbidity maximum associated with the landward extent of the salinity intrusion that is positioned over the Frankfort Flats reach during average discharge and tidal conditions. This turbidity maximum may be responsible for a patch of fine sediments in the Frankfort Flats reach in an otherwise coarse-grained bed. Additional transport and trapping of fine sediments within this reach is the result of secondary circulation driven by centripetal acceleration around meanders in the channel. Close proximity of meanders at Frankfort Flats, within ~5 km, creates opposite secondary circulation of magnitude ~0.2 m/s during flood and ebb conditions. / Thesis (BS) — Boston College, 2011. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Geology & Geophysics Honors Program. / Discipline: Earth and Environmental Sciences.

O aporte de sedimento fino é um dos principais agentes causadores de impactos a ecossistemas aquáticos. Este trabalho teve por finalidade avaliar por experimentalmente o efeito do sedimento fino sobre a fauna de macroinvertebrados bentônicos em um riacho subtropical. O local escolhido foi o rio Forqueta no distrito de Barra do Ouro pertencente ao município de Maquiné, RS. Foi adicionado por tratamento cerca 3138 cm3 de sedimento fino, separado em duas frações: areia fina (0 mm a 0,250mm) e areia grossa (0,25 mm a 1mm), em dois níveis, com e sem sedimento. Os dados foram analisados através por meio de uma Análise de Variância (ANOVA) de dois fatores para abundância total, riqueza e riqueza rarefeita, além de uma Análise de Variância Multivariada (MANOVA) para abundância relativa e composição de espécies e de uma Análise de Correspondência Canônica (pCCA), esta última, para avaliar o quanto eventos de perturbações influenciam a fauna aquática. A interação entre a velocidade do fluxo e os fatores envolvendo sedimentos também foram avaliados. O sedimento fino afetou negativamente a abundância total, a riqueza e a composição de espécies, mas não a riqueza rarefeita e a abundância relativa.O fluxo foi um importante fator para a distribuição da fauna avaliada, sendo a abundância, riqueza e a riqueza rarefeita maior em áreas com maior fluxo. Houve interação do fluxo com a areia fina, aumentando seu efeito sobre a abundância total e riqueza rarefeita em locais com maior velocidade de fluxo. A pCCA mostrou que eventos pontuais e de curta duração de acréscimo de sedimento fino não são danosos à fauna aquática. Os resultados obtidos mostram que o sedimento fino afeta de forma negativa a fauna de macroinvertebrados bentônicos em riachos, e este efeito negativo se dá por diversas formas, tais como redução do hábitat, perda da qualidade do alimento, estresse fisiológico e por outros. A relação da fauna com a velocidade pode ser atribuída às preferênciasecológicas dos grupos encontrados. Por alguns resultados divergirem de estudos prévios, o efeito do sedimento fino sobre a fauna aquática deve ser mais bem estudado. / One of the main forms by which aquatic ecosystems are impacted is the input of fine sediment. The objective of our study was to determinate by one experiment the effect of fine sediment on benthic macroinvertebrates in subtropical streams. The study area was the Forqueta River in Barra do Ouro district of Maquiné city, Rio Grande do Sul, Brazil. It’s was added 3138 cm3 of sediment, in two fractions: fine sand (0mm – 0.25mm) and coarse sand (0.25mm – 1mm) into the river with two levels (with or without sediment) . The data were analyzed by Analysis of Variance (ANOVA two-way) for abundance, richness and rarefied richness, the last one intended to compare species richness based on an equivalent number of individuals. Using Multivaried Analysis of Variance (MANOVA) we examined the effect of fine sediment on relative abundance and composition of species. Sediment was used as one factor in four levels. A Partial Canonical Correspondence Analysis (pCCA) was used to examine the effect of the disturbance event on communities. The interaction between the flow and the factors of the sediment was examined. There was a negative effect of fine sediment on abundance, richness and species composition, but the effect was null on relative abundance and rarefaction of species richness. The flow was important for distribution of individuals colleted. The abundance, species richness and rarefied richness were highest on places with fastest flows. The flow increased the effect of fine sand on abundance and rarefied richness. The pCCA showed that disturbance events of small frequency consisting of input of terrestrial sediment have no negative effects on benthic macroinvertebrate. The relationship between flow and benthic macroinvertebrates can be attributed to the ecological preferences of species. These results showed that fine sediment impact is harmful for benthic macroinvertebrates in streams, particularly in termsof abundance. This negative effect may be a consequence of loss of habitat, reduced food quality, physiological stress and others forms. Because some results differ from other studies, the effect of the fine sediment on the benthic macroinvertebrates needs to be better studied.

O aporte de sedimento fino é um dos principais agentes causadores de impactos a ecossistemas aquáticos. Este trabalho teve por finalidade avaliar por experimentalmente o efeito do sedimento fino sobre a fauna de macroinvertebrados bentônicos em um riacho subtropical. O local escolhido foi o rio Forqueta no distrito de Barra do Ouro pertencente ao município de Maquiné, RS. Foi adicionado por tratamento cerca 3138 cm3 de sedimento fino, separado em duas frações: areia fina (0 mm a 0,250mm) e areia grossa (0,25 mm a 1mm), em dois níveis, com e sem sedimento. Os dados foram analisados através por meio de uma Análise de Variância (ANOVA) de dois fatores para abundância total, riqueza e riqueza rarefeita, além de uma Análise de Variância Multivariada (MANOVA) para abundância relativa e composição de espécies e de uma Análise de Correspondência Canônica (pCCA), esta última, para avaliar o quanto eventos de perturbações influenciam a fauna aquática. A interação entre a velocidade do fluxo e os fatores envolvendo sedimentos também foram avaliados. O sedimento fino afetou negativamente a abundância total, a riqueza e a composição de espécies, mas não a riqueza rarefeita e a abundância relativa.O fluxo foi um importante fator para a distribuição da fauna avaliada, sendo a abundância, riqueza e a riqueza rarefeita maior em áreas com maior fluxo. Houve interação do fluxo com a areia fina, aumentando seu efeito sobre a abundância total e riqueza rarefeita em locais com maior velocidade de fluxo. A pCCA mostrou que eventos pontuais e de curta duração de acréscimo de sedimento fino não são danosos à fauna aquática. Os resultados obtidos mostram que o sedimento fino afeta de forma negativa a fauna de macroinvertebrados bentônicos em riachos, e este efeito negativo se dá por diversas formas, tais como redução do hábitat, perda da qualidade do alimento, estresse fisiológico e por outros. A relação da fauna com a velocidade pode ser atribuída às preferênciasecológicas dos grupos encontrados. Por alguns resultados divergirem de estudos prévios, o efeito do sedimento fino sobre a fauna aquática deve ser mais bem estudado. / One of the main forms by which aquatic ecosystems are impacted is the input of fine sediment. The objective of our study was to determinate by one experiment the effect of fine sediment on benthic macroinvertebrates in subtropical streams. The study area was the Forqueta River in Barra do Ouro district of Maquiné city, Rio Grande do Sul, Brazil. It’s was added 3138 cm3 of sediment, in two fractions: fine sand (0mm – 0.25mm) and coarse sand (0.25mm – 1mm) into the river with two levels (with or without sediment) . The data were analyzed by Analysis of Variance (ANOVA two-way) for abundance, richness and rarefied richness, the last one intended to compare species richness based on an equivalent number of individuals. Using Multivaried Analysis of Variance (MANOVA) we examined the effect of fine sediment on relative abundance and composition of species. Sediment was used as one factor in four levels. A Partial Canonical Correspondence Analysis (pCCA) was used to examine the effect of the disturbance event on communities. The interaction between the flow and the factors of the sediment was examined. There was a negative effect of fine sediment on abundance, richness and species composition, but the effect was null on relative abundance and rarefaction of species richness. The flow was important for distribution of individuals colleted. The abundance, species richness and rarefied richness were highest on places with fastest flows. The flow increased the effect of fine sand on abundance and rarefied richness. The pCCA showed that disturbance events of small frequency consisting of input of terrestrial sediment have no negative effects on benthic macroinvertebrate. The relationship between flow and benthic macroinvertebrates can be attributed to the ecological preferences of species. These results showed that fine sediment impact is harmful for benthic macroinvertebrates in streams, particularly in termsof abundance. This negative effect may be a consequence of loss of habitat, reduced food quality, physiological stress and others forms. Because some results differ from other studies, the effect of the fine sediment on the benthic macroinvertebrates needs to be better studied.

Ce travail de thèse porte sur la dynamique des matériaux en suspension (MES) dans des rivières aménagées de montagne, l'Arc en Maurienne et l'Isère. Un des modes de gestion de l'envasement des différents ouvrages hydro-électriques de l'Arc consiste à réaliser des chasses de barrage annuellement. Lors de ces chasses hydrauliques, les sédiments remobilisés du fond des retenues sont transportés à l'aval des ouvrages sur plusieurs dizaines de kilomètres. L'enjeu est alors de quantifier la propagation en aval de ces MES, afin de comprendre l'impact des chasses de barrage sur le lit de la rivière. Dans une première partie, des données de concentration en MES et de débit, mesurées pendant les chasses de barrage de l'Arc entre 2006 et 2012, sont analysées, critiquées et complétées. A partir de ce jeu de données, des cartes spatiales de flux de MES générés par les chasses de barrage sont dressées, et mettent en évidence des répartitions de zones de dépôt et d'érosion. L'incertitude liée au calcul de ces bilans de masse est quantifiée, et les dynamiques de reprise et de dépôt sont discutées. A titre de comparaison, cette méthode a été appliquée à d'autres événements de crues naturelles et de laves torrentielles, pré-échantillonnées à partir de chroniques de mesures en continu. Enfin, pour mieux caractériser les MES transportées pendant ces épisodes de chasse, des mesures complémentaires de granulométrie et de vitesse de chute ont été réalisées quasiment in situ pendant les chasses de 2011 et 2012. Les dynamiques spatiale et temporelle des ces grandeurs permettent d'établir une stratégie de paramétrisation de modèle numérique. La modélisation numérique hydrosédimentaire 1D fait l'objet de la seconde partie de ce travail de thèse. Le code de calcul d'hydraulique à surface libre MASCARET a été utilisé pour modéliser les écoulements générés par les chasses de barrage entre 2006 et 2012. Cette modélisation hydraulique met en évidence le rôle joué par la présence de bancs alternés de rugosités différentes dans le lit de la rivière. Le code de calcul COURLIS, couplé à MASCARET, a été modifié pour modéliser le transport sédimentaire en suspension. Pour prendre en compte la modélisation du transport de MES en lit composé, une méthode d'estimation d'une concentration moyenne par lit est proposée à partir de données issues de la littérature. Le nouveau modèle ainsi obtenu est comparé avec le modèle homogène dans la section sur des cas réels de crue (mai 2010) et de chasses de barrage (2010, 2011 et 2012). Les résultats de modélisation montrent la capacité du nouveau modèle à reproduire les flux mesurés dans les plages d'incertitude calculées, sans avoir recours à une calibration non physique des paramètres. / This phd thesis focuses on the dynamics of suspended sediments in hardness mountain rivers, specifically along the Arc and Isere River. Due to the silting in the Arc reservoirs, dam flushing are conducted annually. During these flushing events, the sediments eroded from the reservoirs are transported downstream over several tens of kilometers. The challenge is then to quantify the downstream propagation of the suspended sediments to understand the impact of dam flushing on the river bed. In the first part, data of suspended sediment concentration and flow discharges, measured during the dam flushing between 2006 and 2012, are analyzed, criticized and completed. From this dataset, spatial distributions of suspended sediment fluxes are presented, as well as specific locations of deposition or erosion areas. To better characterize the suspended sediments during these dam flushing, additional measurement of particle sizing and settling velocity have been made in situ. The spatial and temporal dynamics of these measured values forms the basis for a parameterization strategy of a numerical model. This is the topic of the second part of this phd thesis. A one dimensional hydraulic model, MASCARET, developed over 20 years by EDF R & D, has been used to model discharges during dam flushing between 2006 and 2012. COURLIS, a one dimensional numerical code for suspended sediment transport, also developed by EDF R & D , has been chosen to model the sediment transport dynamic, coupled with MASCARET . To take into account the sediment transport modeling in compound channel, a new method of estimating the average concentration in both main channel and floodplain is proposed, based on data from the literature. The new model thus obtained is compared with the previous one on real case of natural flood and three dam flushing events.

O aporte de sedimento fino é um dos principais agentes causadores de impactos a ecossistemas aquáticos. Este trabalho teve por finalidade avaliar por experimentalmente o efeito do sedimento fino sobre a fauna de macroinvertebrados bentônicos em um riacho subtropical. O local escolhido foi o rio Forqueta no distrito de Barra do Ouro pertencente ao município de Maquiné, RS. Foi adicionado por tratamento cerca 3138 cm3 de sedimento fino, separado em duas frações: areia fina (0 mm a 0,250mm) e areia grossa (0,25 mm a 1mm), em dois níveis, com e sem sedimento. Os dados foram analisados através por meio de uma Análise de Variância (ANOVA) de dois fatores para abundância total, riqueza e riqueza rarefeita, além de uma Análise de Variância Multivariada (MANOVA) para abundância relativa e composição de espécies e de uma Análise de Correspondência Canônica (pCCA), esta última, para avaliar o quanto eventos de perturbações influenciam a fauna aquática. A interação entre a velocidade do fluxo e os fatores envolvendo sedimentos também foram avaliados. O sedimento fino afetou negativamente a abundância total, a riqueza e a composição de espécies, mas não a riqueza rarefeita e a abundância relativa.O fluxo foi um importante fator para a distribuição da fauna avaliada, sendo a abundância, riqueza e a riqueza rarefeita maior em áreas com maior fluxo. Houve interação do fluxo com a areia fina, aumentando seu efeito sobre a abundância total e riqueza rarefeita em locais com maior velocidade de fluxo. A pCCA mostrou que eventos pontuais e de curta duração de acréscimo de sedimento fino não são danosos à fauna aquática. Os resultados obtidos mostram que o sedimento fino afeta de forma negativa a fauna de macroinvertebrados bentônicos em riachos, e este efeito negativo se dá por diversas formas, tais como redução do hábitat, perda da qualidade do alimento, estresse fisiológico e por outros. A relação da fauna com a velocidade pode ser atribuída às preferênciasecológicas dos grupos encontrados. Por alguns resultados divergirem de estudos prévios, o efeito do sedimento fino sobre a fauna aquática deve ser mais bem estudado. / One of the main forms by which aquatic ecosystems are impacted is the input of fine sediment. The objective of our study was to determinate by one experiment the effect of fine sediment on benthic macroinvertebrates in subtropical streams. The study area was the Forqueta River in Barra do Ouro district of Maquiné city, Rio Grande do Sul, Brazil. It’s was added 3138 cm3 of sediment, in two fractions: fine sand (0mm – 0.25mm) and coarse sand (0.25mm – 1mm) into the river with two levels (with or without sediment) . The data were analyzed by Analysis of Variance (ANOVA two-way) for abundance, richness and rarefied richness, the last one intended to compare species richness based on an equivalent number of individuals. Using Multivaried Analysis of Variance (MANOVA) we examined the effect of fine sediment on relative abundance and composition of species. Sediment was used as one factor in four levels. A Partial Canonical Correspondence Analysis (pCCA) was used to examine the effect of the disturbance event on communities. The interaction between the flow and the factors of the sediment was examined. There was a negative effect of fine sediment on abundance, richness and species composition, but the effect was null on relative abundance and rarefaction of species richness. The flow was important for distribution of individuals colleted. The abundance, species richness and rarefied richness were highest on places with fastest flows. The flow increased the effect of fine sand on abundance and rarefied richness. The pCCA showed that disturbance events of small frequency consisting of input of terrestrial sediment have no negative effects on benthic macroinvertebrate. The relationship between flow and benthic macroinvertebrates can be attributed to the ecological preferences of species. These results showed that fine sediment impact is harmful for benthic macroinvertebrates in streams, particularly in termsof abundance. This negative effect may be a consequence of loss of habitat, reduced food quality, physiological stress and others forms. Because some results differ from other studies, the effect of the fine sediment on the benthic macroinvertebrates needs to be better studied.