Les travaux présentés dans ce manuscrit portent sur les courants et le transport de matière solide en suspension, au voisinage de grandes structures immergées en eau peu profonde. Nous avons focalisé notre étude sur le cas de cages d'aquaculture installées dans la rade de Cherbourg. Situées dans une zone de fort courant, elles impactent leur environnement en modifiant l'écoulement et la turbidité locale. En dépit de nombreuses études déjà disponibles sur l'impact hydrodynamique de tels obstacles, de nombreuses questions se posent encore concernant l'écoulement sous la cage, la production de turbulence, l'érosion du sol et la remise en suspension de sédiments, ainsi que le devenir des déchets produits par la cage. Nous avons choisi de développer trois approches complémentaires pour apporter des éléments de réponse à ces questions. La thèse débute par une étude purement théorique de l'hydrodynamique au voisinage d'un obstacle immergé, assimilé à un milieu poreux, et dans une géométrie simplifiée. Ce modèle bi-dimensionnel, dans le plan vertical, donne de premiers ordres de grandeurs concernant la chute de pression motrice le long du courant, l'accélération du fluide sous la cage, la production de turbulence. Cette étude est suivie d'une analyse numérique de ce même modèle, dans laquelle certaines approximations seront levées. En particulier, le modèle numérique permet de considérer des cages plus imperméables que celles analysées par le modèle théorique. Il est cependant limité en nombre de Reynolds, et a été appliqué avec des échelles réduites. Ce modèle numérique a permis d'analyser le lien direct entre le coefficient de traînée effectif de la cage et diverses quantités-clés : le débit à travers la cage, la chute de pression le long du courant, la production de turbulence et l'apparition d'une zone de recirculation à l'arrière de l'obstacle. Ce dernier effet, visible seulement pour des cages très imperméables, a un impact notable sur le transport de sédiments et d'effluents : lorsque l'arrière de la cage devient une zone morte (zone de recirculation), l'essentiel du débit passe au dessous, ce qui crée de fortes survitesses et produit de la turbulence. Celle-ci peut alors entraîner des particules indésirables dans la zone morte, ce qui augmente notablement la complexité de leurs trajectoires et retarde leur évacuation. Enfin, ces études théoriques ont été complétées par des mesures vélocimétriques et turbidimétriques à l'amont et à l'aval d'une grande cage installée dans la rade de Cherbourg. Celles-ci confirment la présence d'une survitesse en provenance du dessous de la cage, comparable à celle prédite par le modèle théorique. Dans le cas d'une cage très peu perméable, la persistence d'une forte turbidité a été mesurée à l'aval de celle-ci, en accord qualitatif avec les simulations numériques. / This manuscript presents investigations of current and sediment transport in the vicinity of large immersed structures in shallow water flows. It focuses on aquaculture cages installed in the roadstead of Cherbourg. Being located in a high stream zone, these obstacles have a non-negligible effect on currents as well as turbidity. In spite of numerous references on this topic, many questions still arise concerning the environmental impact of such objects. Quantitative information are still needed about the flow below the cage, turbulence production, erosion of the sand bed, sediments resuspension, and evacuation of effluents. To deal with these open questions, we have chosen to develop three complementary approaches. The thesis starts with an analytical study of the flow in a simplified two-dimensional model containing a large rectangular porous structure. Only the motion in the vertical mid-plane of the obstacle is considered. This preliminary model provides estimations of various dynamic quantities, like the velocity increase below the cage, the decay of piezometric pressure along the stream, and turbulence production. Then follows a numerical analysis of the very same flow, based on less stringent approximations. Because of the high cost of computations, simulations have been done at a reduced scale. Nevertheless, they confirm most of the findings of the analytical approach for very permeable cages, and provide crucial information also about weakly permeable cages which were out of reach of the analytical model. In particular, the formation of a recirculation cell behind such cages, together with turbulence production, have been studied with the numerical model. This effect has been observed to affect sediment and effluent transport: when the flow at the rear of the cage takes the form of a cell with closed streamlines, the cage can be thought of as closed and most of the flow passes below. This creates large velocity gradients and produces turbulence which significantly increases the dispersion of sediments and effluents. These particles are then likely to be captured for some time in the cell, instead of being evacuated away. In addition to these theoretical approaches, in-situ current and turbidity measurements have been performed upstream and downstream of a large cage immersed in the roadstead of Cherbourg. They confirm the existence of a fast stream emerging from below the cage. Vertical streamwise velocity profiles have been shown to agree with theoretical ones, in the case of a very permeable cage. Also, large turbidity levels have been recorded at the rear of a weakly permeable cage, in qualitative agreement with simulations.

The purpose of the paper was to evaluate the effects of the restoration efforts in Juktån on the plant species richness and composition, vegetation zonation and soil composition. The restoration involved implementation of a dynamic flow, in addition to hydro-geomorphological alterations. Three sites were inventoried in the bypass reach, representing one reach affected only by flow restoration and two reaches affected both by flow and morphological restoration, along with an upstream reference reach unaffected by regulation. Inventories were conducted along an elevational gradient perpendicular to the water and involved occurring species, plant cover, bare ground and soil composition. The results showed a change in species composition after restoration. Riparian associated species were more common after restoration and the proportions of herbs and graminoids increased. Higher flooding caused a change in zonation, increasing the graminoid, riparian forest and amphibious zones along the riparian habitat. Species richness, as well as soil composition remained largely the same. The effects of the hydro-geomorphological alterations were hard to interpret due to lack of data. The results indicate a positive effect of the new flow on the plant species community in the bypass reach, whilst also highlighting the hydro-geomorphologically altered locations as biodiversity hotspots. Time-delay in ecological response is acknowledged as driving factor for the indifference in species richness and soil composition. The hydrological restoration is concluded to be an effective way of simulating natural flow regimes, improving ecological integrity of riparian communities and structural vegetational patterns in the riparian zone of bypass reaches.

River environments are complex and dynamic ecosystems, and provide valuable ecosystem services such as clean water. The species rich riparian vegetation performs many important ecosystem functions such as reducing erosion and filter inputs from upland areas. Regulated flow regimes have decreased riparian plant species richness, cover and plant performance. To restore the integrity of riparian ecosystems, mitigation measures such as re-regulation of water-level regimes toward more natural seasonal fluctuations may be needed. The aim of this study was to assess potential responses of riparian plants to changes in water-level regulation in run-of-river impoundments to better match natural flow regimes. The elevational extent of plant species on riverbanks of two run-of-river impoundments in the Ume River were surveyed and their probability of occurrence along the gradient of inundation duration was modelled and compared to their distribution in the free-flowing Vindel River. Most species showed similar tolerance to flooding in the Ume and Vindel Rivers. Changes in elevational extent in response to three simulated environmental flow regimes were predicted by using the relationship between plant occurrence and inundation duration. A simulated spring flood and low water levels during the latter part of the growing season is predicted to result in the largest increase in elevational extent, with increases of 70-80% for several riparian species. However, only 47% of the riverbanks along run-of-river impoundments in the Ume River is deemed to be suitable for plant establishment, since many riverbanks are steep and devoid of fine-grained substrate as a result of erosion. / Älvmiljöer utgör komplexa och dynamiska ekosystem som tillhandahåller värdefulla ekosystemtjänster så som rent vatten. Den artrika strandvegetation bidrar till många viktiga ekosystemsfunktioner som närings- och giftupptag och till minskad erosion. Vattenregleringen med förändrade flödesregimer har minskat artrikedom, täckningsgrad och tillväxt av strandväxter. För restaurering av strandekosystemen kan omreglering till mer naturliga säsongsvariationer i vattenståndet vara nödvändigt. Den här studien syftade till att förutsäga hur utbredningen av strandväxter längs stränder i vattenkraftsmagasin potentiellt skulle förändras vid användande av miljöanpassade flöden för att mer likna naturliga flödesregimer i outbyggda älvar. Jag undersökte växternas utbredning i höjdled på stranden längs två magasin i Umeälven och beräknade sannolikheten för varje arts förekomst längs strandens översvämningsgradient. Av de arter som förekom i både Umeälven och den närliggande, outbyggda Vindelälven jämfördes växternas utbredningsgränser i respektive älv. De flesta arterna uppvisade liknande översvämningstolerans i Umeälven och Vindelälven. För att förutsäga förändringar i utbredning som respons på tre olika simulerade miljöanpassade vattenståndsregimer, jämfördes arternas översvämningstolerans vid nuvarade vattenstånd med simulerade vattenståndsregimer. En simulerad vårflod och lågt vattenstånd under sensommaren förväntas ge de största responserna i artutbredning med ökningar på 70-80% för ett flertal strandväxter. Endast 47% av älvstränderna i magasinen i Umeälven bedöms vara lämpliga för växtetablering eftersom stora delar av strandsträckorna är branta och saknar finkornigt substrat till följd av erosion.

Floods are major disturbance events for riverine ecosystems, directly and indirectly impacting organisms and their habitat. In this study I investigated the role of riverine floods and flow alteration in regulating aquatic macroinvertebrate population and community structure. I examined this problem using a variety of methods: a meta-analytic review of primary studies from the literature, a mathematical model synthesizing population and flood ecology, a multi-year experimental flood program in an arid-land river, and a field investigation of flood recovery behaviors in a charismatic larval odonate. I found that floods significantly reduced invertebrate abundance in the short term, but had varied effects across particular study sites, microhabitats, and taxonomic groups. I determined that both resistant and resilient capabilities are important to persistence of invertebrate populations after disturbance events, and that these traits may act in a binary fashion. Recovery over time of invertebrate populations may be partially due to "hidden resistance" of spatially displaced individuals in side-channels, benthic substrate, and vegetation or wood. Some invertebrates adapted to flood-prone rivers may possess behavioral adaptations for returning to the main-channel of the river after flood events. This dissertation contributes to riverine disturbance ecology and provides information useful to prediction and management of ecosystem flows in rivers. / Graduation date: 2012

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Adequate water for ecosystems and humans is at a premium as the global population increases and the climate changes. Coping with these impacts requires tools to improve water governance and water management through legal or policy mechanisms. Water governance generates laws, policies, and rulings and water management implements those laws, policies, and rulings and rulings through management decisions. A key concern of water governance is balancing human and ecosystem water needs. Effective governance that promotes sustainable use of water resources to maintain ecosystem integrity is challenging. Many regions do not have sufficient resources for water management or water for ecosystems is not protected under traditional legal mechanisms. The challenge of improving water governance for ecosystems is, therefore, twofold. First, there is a need to provide resources that build the capacity of water managers to allocate water to ecosystems. Second, mechanisms to promote effective transformation of environmental flow needs into policy or practice are required. This research provides methods to advance water management by: 1) assessing environmental flow needs through creation of a geospatial database and 2) improving stakeholder engagement through lessons learned from three multi-year stakeholder engagement processes. Appendix A describes the current understanding of the link between hydrology and riparian and aquatic ecosystems in Arizona through synthesis of environmental flow needs. The synthesized information, stored in a geospatial database, can be used by water managers to determine the water needs to maintain riparian and aquatic habitats. Review of 121 studies reveals that there are very few analyses of surface water and groundwater requirements for intermittent or ephemeral river systems, and there are only limited generalizable data for aquatic species. This database can be used to identify critical geographic and topical knowledge gaps, as well as serve as a single place for water and land managers to assess and use the most current research to inform management decisions. Appendix B provides an empirical example of engagement to promote social learning as a way to preserve water for the environment when law does not protect environmental flows. Through 43 focus groups with 226 individuals representing a diversity of interests, we determined that there was common ground on concerns about water conservation, cooperation, financial incentives, and multiple benefits for water use. Through this engagement process, we found that identifying and then building common ground requires attention to details. These details include the process of analyzing qualitative data and methods for displaying complex information, which are not frequently discussed in the social learning or stakeholder engagement literature. Appendix C presents a framework for designing effective stakeholder engagement based on the experiences of the University of Arizona Water Resources Research Center in three separate processes that engaged water experts. The proposed framework provides an iterative and flexible approach centered on a bridging organization that can bring people together and keep the engagement process moving forward. As illustrated through an evaluation of the three projects, the proposed framework provides for inclusivity, interactiveness, and flexibility in engagement through guidance by a steering committee and iteratively examining the water resource management problem. While further assessment is necessary, it appears that this framework is general enough to be applicable across projects at three different scales and with three separate sets of goals, yet detailed enough to provide a tangible approach that could aid other processes where the goal is implementing and evaluating expert engagement to solve complex problems and promote social learning. Previous studies on water governance have focused predominantly on the identification of the current problems with governance. However, because humans have an important role in shaping the global water cycle, the time has come to focus on solutions. In order to further water management solutions, a better understanding of the tools needed to manage water for ecosystems and effective methods for co-producing knowledge or encouraging social learning are needed. This research provides a regional example of approaches to advance water management using a tool to assess environmental flows needs and frameworks for promoting common ground and social learning in stakeholder engagement.

Increasing demand and competition for freshwater is threatening instream uses including ecosystem services and aquatic habitat. A standard method of evaluating impacts of alternative water management scenarios on instream habitat is Instream Flow Incremental Methodology (IFIM). The primary outputs of IFIM studies are: 1) habitat rating curves that relate habitat availability to streamflow for every species, lifestage, or recreational use modelled; and 2) habitat time series under alternative water management scenarios. We compiled 428 habitat rating curves from previous IFIM studies across 11 rivers in Virginia and tested the ability to reduce this number based on similarities in flow preferences and responses to flow alteration. Individual site-species combinations were reduced from 428 objects to four groups with similar seasonal habitat availability patterns using a hierarchical, agglomerative cluster analysis. A seasonal habitat availability (SHA) ratio was proposed as a future indicator of seasonal flow preferences. Four parameters calculated from the magnitude and shape of habitat rating curves were proposed as response metrics that indicate how a lifestage responds to flow alteration. Univariate and multivariate analyses of variance and post-hoc tests identified significantly different means for the SHA ratio, QP (F=63.2, p<2e-16) and SK (F=65.6, p<2e-16). A reduced number of instream flow users can simplify the incorporation of aquatic habitat assessment in statewide water resources management. / Master of Science

This project focused on the relationship between instream flows and smallmouth buffalo (Ictiobus bubalus) recruitment in the Gulf Coastal Plain of Texas. The flow regime is the dominant factor in lotic systems and, consequently, the relationship between instream flows, including impacts to natural flow regimes, and life-history is a subject of growing interest. Smallmouth buffalo is a good model to investigate the relationship between river flows and variable interannual recruitment success of periodic life-history strategist fish species. Smallmouth buffalo were collected from the Brazos, Colorado, and Guadalupe Rivers of Texas, U.S.A., and otoliths were extracted from individuals in the field and sectioned and photographed in the lab. Photographs of sectioned otoliths were used to estimate age and thus the year in which the individual was spawned by counting back from the time of capture. Population age structure (i.e. a ‘state' or condition at a point in time) was used to infer effects of flow variation on a rates-based process (i.e. recruitment). After controlling for mortality using recruitment index values, interannual variation in recruitment was modeled using multiple components of the flow regime quantified as indicators of hydrologic alteration (IHA) variables based on daily discharge data from USGS gaging stations in each river system. Model selection followed a two-tier approach, first fitting models using only flow attributes associated with the spawning season then adding additional informative parameters from the pre-spawn and post-spawn periods. The primary finding from model selection was that duration of high flow pulses during the spawning season is a critical component of the flow regime associated with successful Smallmouth Buffalo recruitment. These findings have implications for river management and conservation of ecological integrity, in particular populations of periodic life-history strategist species.

abstract: Climate change has the potential to affect vegetation via changes in temperature and precipitation. In the semi-arid southwestern United States, heightened temperatures will likely lead to accelerated groundwater pumping to meet human needs, and altered storm patterns may lead to changes in flood regimes. All of these hydrologic changes have the potential to alter riparian vegetation. This research, consisting of two papers, examines relationships between hydrology and riparian vegetation along the Verde River in central Arizona, from applied and theoretical perspectives. One paper investigates how dominance of tree and shrub species and cover of certain functional groups change along hydrologic gradients. The other paper uses the Verde River flora along with that river's flood and moisture gradients to answer the question of whether functional groups can be defined universally. Drying of the Verde River would lead to a shift from cottonwood-willow streamside forest to more drought adapted desert willow or saltcedar, a decline in streamside marsh species, and decreased species richness. Effects drying will have on one dominant forest tree, velvet ash, is unclear. Increase in the frequency of large floods would potentially increase forest density and decrease average tree age and diameter. Correlations between functional traits of Verde River plants and hydrologic gradients are consistent with "leaf economics," or the axis of resource capture, use, and release, as the primary strategic trade-off for plants. This corresponds to the competitor-stress tolerator gradient in Grime's life history strategy theory. Plant height was also a strong indicator of hydrologic condition, though it is not clear from the literature if plant height is independent enough of leaf characteristics on a global scale to be considered a second axis. Though the ecohydrologic relationships are approached from different perspectives, the results of the two papers are consistent if interpreted together. The species that are currently dominant in the near-channel Verde River floodplain are tall, broad-leaf trees, and the species that are predicted to become more dominant in the case of the river drying are shorter trees or shrubs with smaller leaves. These results have implications for river and water management, as well as theoretical ecology. / Dissertation/Thesis / M.S. Plant Biology 2011

xviii, 128 p. : ill. (some col.) / This dissertation investigates the potential impacts of canals and small dams on gravel-bed rivers and methods for documenting those impacts. First, I evaluate the potential for mapping channel depths along the McKenzie River, OR, using 10 cm resolution optical aerial imagery with a hydraulically-assisted bathymetry (HAB-2) model. Results demonstrate that channel depths can be accurately mapped in many areas, with some imagery limitations. The HAB-2 model works well in the majority of the river (R 2 =0.89) when comparing modeled to observed depths, but not in areas of shadow, surface turbulence, or depths >1.5 m. Next, I analyze the relative effects of a small dam and two diversion canals on sediment distribution along bars of the lower McKenzie River. The typical pattern of downstream fining is disrupted at each feature and several tributaries, particularly in the "reduced water reaches" below canal outtakes. Most modeled discharge values necessary to mobilize bar sediments fall at or below the 2-year flood return interval, with the remaining at or below the 5-year flood return interval, generally reflecting the D 50 values at each bar (20-115 mm). The third analysis investigates the potential to document geomorphic impacts of small dams in Oregon at ecoregion extents using air photos and publically available data sets. This analysis highlights data disparity with respect to the collecting agency's mission and the difficulty of using remote sensing for small dams. Though the imagery was not useful in evaluating small dam impacts due to resolution and feature size, the data were useful in mapping the small dam distribution across Oregon and each ecoregion. Sixty-one percent of Oregon land is located in the catchment of at least one small dam and the greatest number of dams per area is in the Willamette Valley ecoregion. Overall, this research suggests that, while the application of these techniques must be improved, our ability to observe, study, and understand rivers is enhanced by remote sensing advancements and the combined use of these methods in river restoration and management. This dissertation includes previously published and co-authored material. / Committee in charge: W. Andrew Marcus, Chairperson; Patricia F. McDowell, Member; Dan G. Gavin, Member; David W. Hulse, Outside Member