The presence of fine muddy sediment (grain size < 0.1 mm) in streams has many impacts on the fluvial system and those relying on it, both humans and aquatic biota. Previously, fine sediment was considered a washload and has been ignored in transport models. More recently, it has been treated as being transported once the surface gravel layer that stores it is able to be mobilized. We propose that the surface layer need not be mobilized in order for muddy sediment to travel through the fluvial system in a series of erosive and depositional events. Our first study uses a new in situ device to show how mud entrainment from immobile gravel beds behaves cohesionlessly and can be modeled using the framework of classic sand-based models modified to account for hiding effects present in the stream bed. It also provides a method to predict how deep into the surface layer of gravel entrainment of fine sediment will occur given flow and stream bed characteristics. The second study investigates the primary pathway that fine sediment is traveling to get captured within bluehead chub fish nests. It was determined that more deposition of mud occurred in the upstream half of the nest concluding that the primary pathway was hyporheic pumping through the nest. Capture efficiencies of the nests were also found to increase as the length of nests increased. Both of these studies provide supporting evidence in the need to transition modeling fine sediment transport as a series of deposition and resuspension. / Master of Science / Fine muddy sediment (grain size < 0.1 mm) is present in natural streams and has many impacts on the stream system and those relying on it, including humans, plants, animals, and other organisms in the ecosystem. Previously, fine sediment was treated as being too small to consider in models that aid in understanding how a stream transports sediment. This is because small sediment stays suspended in the water column more easily than larger sediment. Therefore, it was just assumed to pass through the system and never deposit into the stream bed. However, in nature we observe large quantities of fine sediment being stored within the stream bed. More recently, it has been assumed that the sediment that does deposit will be transported once the surface gravel layer that stores it is able to be mobilized. That is, the surface gravel layer shields the fine sediment trapped between it and that the mud will stay put until that gravel is moved. We propose that the surface layer need not be mobilized for muddy sediment to travel through the fluvial system in a series of erosive and depositional events. Our first study uses a new device that forces erosion of mud to show how mud entrainment, or the process of how a fluid picks something up and carries it, from immobile gravel beds can be modeled using the framework of classic sand-based entrainment models modified to account for hiding effects, or protection against entrainment of a smaller sediment by a larger sediment shielding it, present in the stream bed. It also provides a method to predict how deep into the surface layer of gravel that fine sediment will be eroded given flow and stream bed characteristics. This is beneficial in estimating the amount of sediment that will be eroded during a given storm event. The second study investigates the primary pathway that fine sediment is traveling to get captured within bluehead chub gravel fish nests used for spawning their eggs and reproducing. It was determined that more deposition of mud occurred in the upstream half of the nest. This leads us to believe that the primary pathway of sediment traveling through the nest was hyporheic pumping through the nest, or the process of water flowing down through the surface layers of sediment in the stream bed. Capture efficiencies, or the ratio of how much of the sediment that traveled through the nest was captured, of the nests were also found to increase as the length of nests in the downstream direction increased. Both of these studies provide supporting evidence in the need to transition modeling fine sediment transport as a series of deposition and resuspension.

Yes / The Three Gorges Dam (TGD) constructed at the Yangtze River, China represents a revolutionary project to battle against the mage-scale flooding problems while improving the local economy at the same time. However, the large-scale fine-size sediment and pollutant material transport caused by the TGD operation are found to be inevitable and long-lasting. In this paper, a multi-fluid Incompressible Smoothed Particle Hydrodynamics (ISPH) model is used to simulate the multi-fluid flows similar to the fine sediment materials transport (in muddy flows) and water flow mixing process. The SPH method is a mesh-free particle modeling approach that can treat the free surfaces and multi-interfaces in a straightforward manner. The proposed model is based on the universal multi-fluid flow equations and a unified pressure equation is used to account for the interaction arising from the different fluid components. A Sub-Particle-Scale (SPS) turbulence model is included to address the turbulence effect generated during the flow process. The proposed model is used to investigate two cases of multi-fluid flows generated from the polluted flow intrusions into another fluid. The computations are found in good agreement with the practical situations. Sensitivity studies have also been carried out to evaluate the particle spatial resolution and turbulence modeling on the flow simulations. The proposed ISPH model could provide a promising tool to study the practical multi-fluid flows in the TGD operation environment. / The Major State Basic Research Development Program (973 program) of China (No. 2013CB036402) and the National Natural Science Foundation of China (No. 51479087).

The freshwater pearl mussel Margaritifera margaritifera is an endangered bivalve which is usually regarded as sedentary, although individual movement has been observed both vertically and horizontally. Little is known about the causes and rates of mussel movement. The objective of this study was to test the effect of microhabitat characteristics on the horizontal movement distance and rates of freshwater pearl mussels. A total of 120 mussels (length range 40–59 mm) were marked individually with passive integrated transponder tags, placed in stream microhabitats differing in their sediment composition and monitored biweekly over a period of 10 weeks. Mussels situated in sand-dominated habitats had a significantly higher mean movement rate (3.2 ± 4.2 cm/day, mean ± SD) than mussels situated in gravel-dominated (1.9 ± 2.7 cm/day) or stone-dominated habitats (1.8 ± 3.2 cm/day). The direction of the movements appeared random; however, an emigration from sandy habitats was observed, probably to avoid dislodgment from these hydraulically unstable habitats. This study demonstrates that freshwater pearl mussels can actively emigrate from unsuitable microhabitats. Once suitable streams with respect to physical, chemical, and biological quality were identified, it is therefore only necessary to identify suitable mesohabitats (area of 10–30 m²) when reintroducing or relocating mussels.

Le but de cette thèse est de comprendre la dynamique des graviers au sein des rivières alpines à faible contrainte en utilisant des expériences en laboratoire. Ces rivières sont souvent composées d’une large gamme de sédiments, allant des argiles aux galets. Ces différentes classes sédimentaires peuvent interagir entre elles, ce qui peut rendre difficile l’estimation du transport solide. Des expériences en laboratoire ont été conduites en écoulements instationnaires dans un canal de 18m de long et 1m de large. Deux types de lits ont été étudiés : lits unimodaux et bimodaux. Une attention particulière a été portée sur la réalisation des lits de graviers dans notre canal. Ils ont été créés dans le but d’approcher au mieux la configuration des lits de rivières alpines, c’est-à-dire avec différents arrangements et degrés de colmatage du lit par des sédiments fins. Les lits unimodaux sont composés de graviers peu triés avec divers arrangements de surface. Les lits bimodaux sont composés d’une matrice de graviers peu triés dans laquelle des sédiments fins se sont infiltrés (sables ou limons). Les processus régissant le transport de graviers ont été mis en avant. Le transport de graviers est impacté par l’arrangement du lit, la concentration de sédiments fins dans la couche de charriage, et par le changement de propriétés du lit due à la présence de sédiments fins (cohésion, perméabilité du lit). Plus le lit est arrangé, plus le transport est difficile. Plus la couche de charriage est concentrée en sédiments fins, plus le transport est facile. La forme des sédiments fins est aussi un facteur important pouvant modifier le transport des graviers. La présence de sédiments fins cohésifs dans la matrice peut considérablement réduire le taux de graviers transportés. Un modèle conceptuel a été développé pour résumer les différents processus contrôlant le transport de graviers. Il décrit le comportement des graviers dans les différentes configurations étudiées. L’outil proposé peut aider à comprendre, estimer et interpréter le transport de graviers. Il a été appliqué et discuté sur un cas de terrain sur la rivière de l’Arc. Basé sur ce modèle, nous avons proposé une nouvelle analyse dimensionnelle pour la construction d’un modèle de prédiction de transport solide prenant en compte des paramètres décrivant l’arrangement du lit, les propriétés géotechniques du lit et la présence de sédiments fins / This PhD thesis aims to understand gravel dynamics in Alpine rivers at low bed shear stress using laboratory experiments. Alpine river beds are often poorly sorted and composed of sediments ranging from clay to pebble. To understand interactions between these classes is an issue for predicting bedload rate. Laboratory experiments were performed in a 18m long and 1m wide flume, under unsteady flows. Two types of bed were investigated: unimodal and bimodal beds. A particular attention was paid to the bed construction, which was conducted in order to obtain a nature-like bed 12with different bed arrangements and degrees of clogging. Unimodal beds were made of moderately sorted gravels with different bed surface arrangements. Bimodal beds were made of moderately sorted gravels in which fine sediments (sand or silt) were infiltrated. Gravel rate was found to be impacted by the bed arrangement degree, the fine sediment concentration within the bedload layer and the changes in bed properties due to fine sediment presence (bed cohesion, bed permeability). The more packed the bed is; the more difficult it is to move gravels. The more concentrated in fine sediment the bedload layer is; the easier the transport of gravels is. The shape of fine sediments can also be an important factor for modifying the gravel rate. The presence of cohesive fine sediments within the bed matrix reduces significantly the gravel rate. A conceptual model was developed to recap the different processes controlling gravel transport. It provides a phenomenological description of the overall bed responses to a hydrograph. This tool is designed to help understanding, estimating or interpreting gravel transport in Alpine rivers. The conceptual model was discussed and applied to a field case made on the Arc River. Using the model, we also suggest a new dimensionless analysis for the construction of a bedload predicting model involving parameters describing bed arrangement, bed properties and fine sediment presence

L’apport de sédiments fins au cours d’eau est un phénomène naturel mais qui sous les effets de l’anthropisation peut devenir excessif et conduire à perturber le fonctionnement de l’hydrosystème. Cet apport excessif provoque le colmatage du lit des rivières et peut perturber les échanges hydriques, les processus biogéochimiques et les communautés d’invertébrés benthiques et hyporhéiques. D’un point de vue méthodologique, la mesure de la conductivité hydraulique dans le substrat permet d’obtenir une image du niveau de colmatage de la zone hyporhéique et le pompage Bou Rouch permet d’étudier qualitativement la faune hyporhéique. D’un point de vue biologique, les effets du colmatage sont un peu plus importants pour l’hyporhéos que pour le benthos notamment au niveau de la richesse taxonomique, des assemblages faunistiques et des traits biologiques / Fine sediment input to the streambeds is a natural phenomenon but in addition to the effects of human impacts may become excessive and lead to disruption of the functioning of the hydrosystem. This excessive intake causes the clogging of river beds and can disrupt water exchange, biogeochemical processes and benthic and hyporheic invertebrate communities. From a methodological point of view, measurement of hydraulic conductivity in the substratum provides a realistic picture of the clogging level of the hyporheic zone and the Bou Rouch pump a good sampling for a qualitative study of the hyporheic fauna. From a biological point of view, the clogging effects on the hyporheos are higher compared to the benthos regarding taxonomic richness, changes in faunal assemblages and biological traits