The spatial and temporal flow field characteristics of a gravel-bed river supporting a robust rainbow trout (Onchorhynchus mykiss) and brown trout (Salmo trutta) fishery were studied in high resolution in attempts to hydraulically quantify the selection preferences and incubation characteristics of redds. Measurements were obtained at both the riffle- and redd-scale post-spawning, in addition to pre- and post-bed mobilization flow events. A Pulse Coherent Acoustic Doppler Profiler (PCADP) was adapted for use in the lotic environment where between 4000 to 5000 three-dimensional velocity measurements could be obtained on a daily basis at the riffle scale. Bed material samples were obtained and scour chains installed to characterise the bed mobility, critical shear, and macro-erosion of each riffle studied. At the riffle-scale, seasonal variability in the mean and variance of commonly used hydrodynamic parameters (velocity, flow depth, Froude number, bed roughness, turbulent kinetic energy per unit area) was often explicitly related to changes in sampling discharge and channel structure. Riffle-scale directional semivariograms isolated varied scales of spatial dependency, and the occurrence of bed mobilizing and channel-forming discharge created a less smooth and poorly defined spatial structure. Redd-scale omnidirectional semivariograms presented the same response to channel-forming discharge, however overall did not reveal a coherent spatial structure. Although the commonly used Froude number did not present patterns or characteristics which could distinguish the redd properties from the riffle, the results for local velocity and turbulence at the redd-scale revealed evidence of optimal physical conditions for salmonid incubation, particularly convective flow acceleration which promotes downwelling at the egg pockets and unidirectional flow with low turbulence, which allows this behaviour to persist through a range in environmental flows.

The spatial and temporal flow field characteristics of a gravel-bed river supporting a robust rainbow trout (Onchorhynchus mykiss) and brown trout (Salmo trutta) fishery were studied in high resolution in attempts to hydraulically quantify the selection preferences and incubation characteristics of redds. Measurements were obtained at both the riffle- and redd-scale post-spawning, in addition to pre- and post-bed mobilization flow events. A Pulse Coherent Acoustic Doppler Profiler (PCADP) was adapted for use in the lotic environment where between 4000 to 5000 three-dimensional velocity measurements could be obtained on a daily basis at the riffle scale. Bed material samples were obtained and scour chains installed to characterise the bed mobility, critical shear, and macro-erosion of each riffle studied. At the riffle-scale, seasonal variability in the mean and variance of commonly used hydrodynamic parameters (velocity, flow depth, Froude number, bed roughness, turbulent kinetic energy per unit area) was often explicitly related to changes in sampling discharge and channel structure. Riffle-scale directional semivariograms isolated varied scales of spatial dependency, and the occurrence of bed mobilizing and channel-forming discharge created a less smooth and poorly defined spatial structure. Redd-scale omnidirectional semivariograms presented the same response to channel-forming discharge, however overall did not reveal a coherent spatial structure. Although the commonly used Froude number did not present patterns or characteristics which could distinguish the redd properties from the riffle, the results for local velocity and turbulence at the redd-scale revealed evidence of optimal physical conditions for salmonid incubation, particularly convective flow acceleration which promotes downwelling at the egg pockets and unidirectional flow with low turbulence, which allows this behaviour to persist through a range in environmental flows.

The aim of this thesis was to improve our understanding of plant – flow interactions and to develop new remote sensing techniques that would allow a marsh scale assessment of flow modification due to the presence of salt marsh vegetation. The limitations of current approaches which improve our understanding and prediction of tidal flows centre around poor assessments of canopy structure and mechanical properties. The validity of such simplified and reductionist assessments of canopy structure were tested and found to contribute considerable error in estimations of canopy frontal area and canopy drag. New metrics to assess canopy structure were tested as part of a flume study using two salt marsh species with varying form and architecture. Results from this experiment found that biomass located immediately below the water surface are important for determining fluid momentum losses in salt marsh canopies. These results led to the development of a new empirical based model using vertical measures of biomass and approach (incident) velocity which can accurately (R2 0.71) predict flow momentum losses. This suggests that the characteristic vegetation parameter and the drag coefficient may be substituted with vertical canopy biomass and an empirical coefficient. This may lead to more accurate assessments of canopy structure and thus comparable results across the literature as well as potentially apriori assignment of parameters in the force drag model. Vertical canopy biomass (3D biomass) was then estimated at the marsh scale using a combined remote sensing approach and an empirical model. Accurate assessments of the marsh surface are critical for hydrodynamic models and important if we are to determine vertical changes in canopy structure. The approach first identified marsh surface returns by operating a moving average smoothing filter on Airborne Laser Scanning (ALS) data. The automated procedure detected vegetated and non–vegetated surfaces using aerial NDVI which calibrated the filter and ensured ALS returns were representative of marsh surface elevation. Using the marsh surface DEM, vegetation was reconstructed at 0.2 m grid cells. Terrestrial Laser Scanning (TLS) was found to accurately quantify maximum canopy height (RMSE 0.14m) whilst a regression model using aerial NDVI and spatial coordinates gave reasonable predictions (RMSE 0.08kg/m2) of total plot canopy biomass within each 0.2 m cell across a ~20,000 m2 area of marsh. Ground measurements found the vertical distribution of canopy biomass followed a power law increase with elevation from the marsh bed. Combining all the approaches allowed the creation of a 3D assessment of canopy biomass with an average error of 30% of the mean amongst plots exhibiting larger canopy biomass ( > 0.4 kg/m2). This vertical measure of biomass can be combined with the flow momentum loss model generated in the flume experiment to assess hydrodynamic canopy drag potential at the marsh scale. Roughness coefficients can also be calculated using this approach which can be easily fed into commercially available numerical flow models.

Recent studies within the past decade or so have shown the importance of algae in geomorphic and hydrologic processes of lotic systems. However, the ecohydraulic role of algae in bedrock systems has largely been ignored. In addition, the utility of algae as indicators of channel dynamics have often been assumed by geomorphologists, but relatively few studies have examined this relationship. The purpose of this study was to determine whether algae, specifically diatoms, are useful indicators of channel geomorphological dynamics, and to examine if distinct habitats or biotopes typical in fluviokarst and bedrock systems provide unique habitat space for diatoms, and to address the potential ecohydraulic implications. The investigation was performed in a 100 m reach of Shawnee Run, a limestone, fluviokarst tributary to the Kentucky River in Mercer County, KY. The results of the study showed that periphyton are not useful indicators of channel dynamics, and that biotopes and other distinct habitats, including riffles, bedforms, and fine sediment, do not provide unique habitat in terms of diatom community composition.

<p>Hyporheic exchange is key to buffer water quality and temperatures in streams and rivers, while also providing localized downwelling and upwelling microhabitats. In this research, the effect of geomorphological parameters on hyporheic exchange has been assessed from a physical standpoint: surface and subsurface flow fields, pressure distribution across the sediment/water interface and the residence time in the bed.<br></p><p>First, we conduct a series of numerical simulations to systematically explore how the fractal properties of bedforms are related to hyporheic exchange.We compared the average interfacial flux and residence time distribution in the hyporheic zone with respect to the magnitude of the power spectrum and the fractal dimension of riverbeds. The results show that the average interfacial flux increases logarithmically with respect to the maximum spectral density whereas it increases exponentially with respect to fractal dimension.<br></p><p>Second, we demonstrate how the Froude number affects the free-surface profile, total head over sediment bed and hyporheic flux. When the water surface is fixed,the vertical velocity profile from the bottom to the air-water interface follows the law of the wall so that the velocity at the air-water interface has the maximum value. On the contrary, in the free-surface case, the velocity at the interface no longer has the maximum value: the location having the maximum velocity moves closer to the sediment bed. This results in increasing velocity near the bed and larger head gradients, accordingly.<br></p><p>Third,we investigate how boulder spacing and embeddedness affect the near-bed hydrodynamics and the surface-subsurface water exchange.When the embeddedness is small, the recirculation vortex is observed in both closely-packed and loosely-packed cases, but the size of vortex was smaller and less coherent in the closely-packed case. For these dense clusters, the inverse relationship between embeddedness and flux no longer holds. As embeddedness increases, the subsurface flowpaths move in the lateral direction, as the streamwise route is hindered by the submerged boulder. The average residence time therefore decreases as the embeddedness increases.<br></p><p>Lastly, we propose a general artificial neural network for predicting the pressure field at the channel bottom using point velocities at different level. We constructed three different data-driven models with multivariate linear regression, local linear regression and artificial neural network. The input variable is velocity in x, y, and z directions and the target variable is pressure at the sediment bed. Our artificial neural network model produces consistent and accurate prediction performance under various conditions whereas other linear surrogate models such as linear multivariate regression and local linear multivariate regression significantly depend on input variable.<br></p><p>As restoring streams and rivers has moved from aesthetics and form to a more holistic approach that includes processes, we hope our study can inform designs that benefit both structural and functional outcomes. Our results could inform a number of critical processes, such as biological filtering for example. It is possible to use our approach to predict hyporheic exchange and thus constrain the associated biogeochemical processing under different topographies. As river restoration projects become more holistic, geomorphological, biogeochemical and hydro-ecological aspects should also be considered.<br></p>

Half the world’s river volume is affected by flow alterations and/or fragmentation, a figure that is likely to increase with the current global surge in hydropower development. At the same time, freshwater biodiversity is in rapid decline. In fluvial ecosystems, streamflow is a master variable, shaping riverine species’ habitat over space and time. Atlantic salmon (Salmo salar) and brown trout (S. trutta) are examples of species that need fluvial habitats for reproduction and juvenile rearing, and whose flow needs can come in conflict with hydropower production objectives. This necessitates tools for predicting the effect of fluvial habitat alteration on fish production. In this thesis, I applied the individual-based model inSTREAM to simulate salmon and trout in the Gullspång Rapids, a residual flow stretch of the Gullspång River, Sweden, over a ten-year period. InSTREAM uses sub-daily time steps to simulate individual fish interacting with their biotic and physical environment, and tracks the fitness consequences of their main actions: habitat and activity selection. For inSTREAM input, I had to describe key habitat features, create a 2D hydraulic model of the rapids, model river temperature, and gather data on salmon and trout eco-physiology and life history characteristics in the Gullspång River. I ran simulation experiments varying either flow input, the number of spawners, spawning gravel, shelter and boulder availability, or temperature. Flow alterations had limited benefit. Only the scenario where the current minimum flow was set three times higher yielded increased production, and only for trout. Trout dominated salmon in competition, and production was density dependent. The model predicted that the only way to increase production of both species at current spawner numbers was to add instream structures offering more energetically profitable feeding positions. / Half the world’s river volume is affected by flow alterations and/or fragmentation –a figure that is likely to increase with the current global surge in hydropower development. Streamflow shapes the river habitat for species like Atlantic salmon (Salmo salar) and brown trout (S. trutta) –species that need rivers for reproduction and for juvenile rearing. In this thesis, I applied the individual-based model inSTREAM to simulate how salmon and trout interact with the physical and living environment in the Gullspång Rapids, a residual flow stretch in the Gullspång River, Sweden. InSTREAM follows individuals through spawning, egg development, and juvenile rearing until out-migration. I ran simulation experiments over ten years, varying either flow input, the number of spawners, spawning gravel, shelter availability, or temperature. Flow alterations had limited benefit; only in the scenario where the current minimum flow was tripled did production increase, and only for trout. Trout dominated salmon in competition for food and space, and production was density dependent. The model predicted that the only way to increase production of both species at current spawner numbers was to add instream structures offering more energetically profitable feeding positions. / <p>Article 2 part of thesis as manuscript, now published.</p>

As all of Sweden's hydropower is to be re-examined within a 20-year period, methods are needed to carry out ecological investigations of dammed waterways. The first aim of this thesis is to evaluate whether methods for salmon and trout habitat mapping take all relevant indicators into account. In addition, the report aims to investigate which factors affect the results of habitat mapping based on hydraulic simulation and to investigate whether this method can be made more efficient through the use of simpler models, drone images and calculations. The work began with a literature study. A model was then built over a dammed stretch where mapping through hydraulic simulation was carried out. A mapping was then carried out on another stretch of stream based on a simpler model, drone images and shadow calculations, in parallel with a field mapping. The results of the literature study showed that the mapping methods capture the physical indicators well and indirectly link to certain chemical and ecological indicators. The method could be improved by including the water's nitrogen content and pH in the assessment.Important factors in habitat estimation with hydraulic simulation are the flow and the accuracy of the terrain model, as well as how the result is produced. The result from mapping with a simpler hydraulic model showed large deviations from the results obtained in the field, with respect above all to depth and width. Drone imagery for substrate assessment works well in shallow and clear water bodies. Shadow calculations based on how they were applied in this work to habitat mapping have not given satisfactory results, why the method needs to be developed. / Då all Sveriges vattenkraft ska omprövas inom en 20-årsperiod behövs metoder för att genomföra ekologiska utredningar av uppdämda vattendrag. Det första syftet med detta examensarbete är att utvärdera om metoder för lax- och öringhabitatkartering tar hänsyn till alla relevanta indikatorer. Därutöver syftar rapporten till att undersöka vilka faktorer som påverkar resultatet vid habitatkartering utifrån hydraulisk simulering och att undersöka om denna metod kan effektiviseras genom användning av enklare modeller, drönarbilder och beräkningar. Arbetet inleddes med en litteraturstudie. Därpå byggdes en modell upp över en indämd sträcka där kartering genom hydraulisk simulering genomfördes. En kartering genomfördes sedan på en annan strömsträcka utifrån en enklare modell, drönarbilder och skuggberäkningar, parallellt med en fältkartering. Litteraturstudiens resultat visade på att karteringsmetoderna väl fångar upp de fysikaliska indikatorerna och indirekt kopplar till vissa kemiska och ekologiska indikatorer. Metoden skulle kunna förbättras genom att ta in vattnets kvävehalt och pH i bedömningen. Viktiga faktorer vid habitatskattning med hydraulisk simulering är flödet och terrängmodellens noggrannhet, samt klassningen för vad som anses som goda habitat. Resultatet från kartering med en enklare hydraulisk modell visar på stora avvikelser mot resultaten inhämtade i fält, med avseende på framför allt djup och bredd. Drönarbilder för substratbedömning fungerar väl vid grunda och klara vattendrag. Skuggberäkningar utifrån hur de i detta arbete applicerats på habitatkartering har inte gett tillfredställande resultat, varför metoden behöver utvecklas.

Un des enjeux de la Directive Cadre sur l'Eau (2000) est de rétablir la migration piscicole aval à travers notamment une baisse de la mortalité des poissons au niveau des turbines des centrales hydroélectriques. Les grilles ichtyocompatibles constituent une des solutions possibles grâce à un arrêt physique des poissons couplé à un guidage vers un exutoire de contournement. Dans ce contexte, nous avons mené une étude expérimentale et numérique afin de caractériser différents types de grilles en termes de pertes de charge et de courantologie. Cela a permis de déterminer d'une part les pertes d'énergie liées à la proximité des barreaux pour diverses configurations et d'autre part les vitesses que les poissons sont susceptibles de rencontrer le long des grilles jusqu'à l'exutoire. Ces deux sujets complémentaires ont été abordés via l'utilisation de deux installations hydrauliques couplées à plusieurs systèmes de mesure adaptés à nos modèles de grille. Des mesures de hauteur d'eau ont permis d'établir des nouvelles lois de pertes de charge tandis que des mesures de vitesse avec des systèmes de vélocimétrie acoustique par effet Doppler (ADV) et de vélocimétrie par images de particules (PIV) ont permis de déterminer les angles pour lesquels les grilles satisfont les critères d'ichtyocompatibilité. Certains points de l'étude, liés à la caractérisation des exutoires notamment, ont été résolus grâce à des simulations numériques avec le logiciel OpenFOAM. L'ensemble des résultats obtenus a permis de dimensionner et de comparer les différentes solutions de grilles dans un cas de prise d'eau réel, soulignant ainsi les avantages et problématiques inhérents à chacune des solutions. / The Water Framework Directive (2000) particularly aimed at restoring the fish downstream migration and at preventing fish from being injured or killed in hydropower plant turbines. Fish-friendly trashracks, which physically stop fish and guide them towards bypasses, are one of the possible solutions.In this context, we have carried out an experimental and numerical study focused on the characterization of head losses and velocity distributions for various kinds of trashrack. This helped to quantify the energy loss due to the narrow bar spacing and to assess the magnitude of velocities that fish may face in different trashrack configurations. Two hydraulic installations coupled with several measurement devices allowed the study of both topics on model trashracks. Water depth measurements resulted in new head loss equations while velocity measurements with acoustic Doppler velocimetry (ADV) and particle image velocimetry (PIV) systems allowed the determination of fish-friendly angles in different trashrack configurations. Some other points of the thesis, concerning for instance bypasses, have been investigated with numerical simulations using OpenFOAM software. All the results allowed the conception and the comparison of various trashrack solutions for a real water intake case, highlighting the advantages and drawbacks relative to each of these solutions.