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With an ever growing population the city of Lausanne has a need to monitor and preserve its main water source, the lake. Permanent discharge from combined sewer over ows (CSO) and the waste water treatment plant have an impact on the Vidy Bay, making it the area the most polluted of the lake (Pote et al., 2008). In this prestudy, we evaluate the impact of the urban wet weather discharge focused on the CSOs, through modelling of sediment transport, as a proxy for pollution (Rossi, 2007b), in commonly observed conditions. The existing hydrodynamic Delft3D Z-model of lake Geneva was adapted to picture sediment transport. After validation of its hydrodynamics on the six rst month of 2014, the resulting deposition/erosion pattern, shear velocity maps and mass balance were analysed. The CSO investigated has two discharge regimes with 90% of discharges under 5 m3/s capable of short range transport, while large discharge for light sediment and strong currents demonstrate long range transport capable of exiting the bay. Hydrodynamics are the main driver of the deposition pattern, leading the sediment plume of the CSO to stretch in multiple direction depending on the wind. Resuspension was identied as a major source of sediment transport events in the bay. These originated from short-, medium- and long-range transport. Over the short period investigated, the region near St-Sulpice was surprisingly identied as a hot spot for suspension in the bay, shaping the modelled deposition pattern after six month in front of the CSO outlet for light sediments. Comparison with in-situ samples from Benejam (2016) show the same zones of in uence for the six months simulated. The proposed and tested modelling approach of this study suggest promising future applications.

A three-dimensional hydrodynamic Z-model was conceived for Lake Zurich (Switzerland, ZH) using the modeling software Delft3D. Calibration was performed on the thermal profile in 2017 at three monitoring stations located in both basins, and was validated on years 2015 and 2016 with the same method. The model reproduced effectively thermal stratification and water temperature’s spatial and temporal variability. Specific hydrodynamic events were correctly simulated: upwellings were detected but their amplitude was underestimated; seiches periods were found accordingly to values reported in the literature. Hypolimneon’s temperature was nicely reproduced but results were less accurate in the epilimneon and especially in the metalimneon. Flow velocities were qualitatively evaluated and exhibited realistic values; the model was able to reproduce clockwise and counterclockwise flow rotation motions. Suggested improvements imply collecting more data about rivers, the importance of the latter on Obersee dynamics having been demonstrated, and the focus on wind drag coefficients in the calibration process.

Freshwater resources play a central role in social and economic development of modern civilisations, yet their value is often underestimated and neglected in developed countries. In fact, freshwater habitats are facing unprecedented threat because of human activities, and it is necessary to provide reliable water quality indicators to monitor the response of aquatic systems. In this context, remote sensing has a great potential to provide a complementary source of data for monitoring and under-standing the processes involved in inland waters around the world at fine temporal and spatial reso-lutions. The scientific approach adopted in this thesis is based on the integration of complementary sources of information provided by state-of-the-art monitoring methods to foster our understanding of freshwater habitats. Specifically, we demonstrate the additional value provided by combining com-plementary sensors with bio-geochemical measurements and hydrodynamic models, using a rare event in Lake Geneva which got a wide public attention in local newspapers: a calcite precipitation event. The principal focus of the remote-sensing community has recently been directed towards very turbid waters in order to address the challenges involved with the retrieval of mixed constituent concentra-tions. In this thesis, I highlight some important challenges relative to clearer waters which also re-quire further attention from the community. Specifically, I provide a solution to account for vertical non-uniformities of water constituent concentrations using simple approximation models in Lake Geneva. Finally, I provide a comprehensive comparison between state-of-the-art atmospheric correction methods, which are presumably relevant for inland water monitoring and applicable to the new con-stellation of remote sensors. The aim is to provide reliable recommendations to help forthcoming studies to apply the most suited procedure to their investigation.

Gravity currents are buoyancy-driven flows having a significant impact on the environment and human life. They can be observed in a vast range of natural and anthropogenic scenarios, such as seawater and freshwater, the atmosphere, or industrial processes. Gravity currents transport sediments, nutrients, and oxygen in water bodies but they are also often dramatically involved in the spreading of contaminants and can represent a severe hazard to humans and infrastructures. The relevance of these phenomena has motivated extensive research on gravity currents such as the present study which addresses two main different research objectives. The first objective of this research concerns the modeling of gravity currents with Shallow Water Equations (SWE). Large Eddy Simulations data of continuously-fed gravity currents are used to discuss how the chosen definition of current depth affects the value of the coefficients appearing in the SW continuity and momentum equations due to the non-uniformity of the vertical distribution of flow variables. Moreover, the implications that different definitions of current depth have on research findings and entrainment parameterization are discussed. This analysis showed that coefficients appearing in the momentum equation might significantly (up to $30\%$) differ from one, depending on the chosen current depth definition. On the contrary, the coefficients appearing in the continuity equation were shown to be very close to one. The second main research objective was to study how the mean and turbulent structure of a density current changes when it propagates over a porous substrate and to characterize the volume exchanges occurring at its lower interface. Experiments were carried out in the Laboratory of Hydraulic Constructions at EPFL to reproduce continuously-fed density (saline) currents, which propagated first over a smooth horizontal bed and then over a porous substrate of limited length. Inflow discharge, initial excess density, substrate porosity, and downstream confinement of the substrate were systematically varied. An image analysis technique was developed to monitor the flow density evolution above the substrate and within its pores. Simultaneously, an Acoustic Doppler Velocimetry Profiler acquires a quasi-instantaneous 3D vertical velocity profile over the substrate. Experimental results showed that, after an initial phase during which the current sinks into the substrate, freshwater entrainment from the substrate pores starts. Consequently, a mixing layer gradually forms at the lower boundary of the current. Its presence affects the mean density, mean velocity, and turbulent field primarily in the near-bed region, where buoyancy contributes to turbulent kinetic energy generation together with shear. Moreover, at the porous substrate interface, buoyancy instabilities enhance the bed-normal momentum flux, increasing the bulk flow resistance. As a consequence, although the no-slip boundary condition results in lower friction losses, the shear velocity increases with the porosity of the substrate. In addition, experimental measurements allowed to quantify the current volume loss and the ambient-fluid entrainment from the substrate pores. The main drivers of these exchanges are discussed. The study of the entrainment of ambient-fluid from the bottom is fundamental to understand and model the resuspension of substances, such as nutrients and pollutants, present in the porous substrates.

When lake surface waters above the temperature of maximum density 4◦C cools, the verysurface fluid parcels become denser than their neighbours below. The latter process leads to a gravitationally unstable density distribution which may trigger ‘free convection’, i.e. the upper denser waters look for their equilibrium position somewhere down in the water column. This phenomenon usually occurs at night time, when the atmosphere is colder than surface waters. However, during daytime, it may happen that the lake surface cools—releasing heat to the atmosphere—while shortwave radiation penetrates through upper waters. In this scenario, the near surface waters of the photic zone can host an unstable layer due to the net surface cooling, whereas waters beneath it experience radiative heating and gravitational stabilization. Here, we investigate the competition between shortwave radiation and surface cooling when wind is low or negligible. Thus, depending on the relative intensity of surface cooling and shortwave radiation, the upper water column undergoes different gravitationally unstable density distributions and potentially convective regions. The objective of this Master Project is to investigate, describe, and characterise such convective regimes. To do so, the heat equation controlling temperature evolution of the upper water column subject to surface cooling and penetrative radiative heating is investigated. In parallel with in-situ observations, mathematical and numerical modelling allow to understand the phenomenon taking place. The results allow to infer how the relative importance of surface cooling and penetrating shortwave radiation may affect vertical heat and mass transfer within the lake and between the lake and the atmosphere.

Base Mine Lake (BML) is a pit lake used to store the Fluid Fine Tailings (FFT) generated by the oil sands industry, in the Athabasca region (northern Alberta, Canada). It is well studied to try understanding its evolution over time and to determine if an effective separation of the FFT from the cap water will eventually be reached. The mixing mechanisms taking place in the lake and affecting the suspended solids are of particular interest. Turbidity increases at the bottom of the water column suggesting the presence of a turbid layer which might be subject to mixing. The solids concentration exceeds the maximum limit of the sensors and deeper values cannot be recorded which prevents to fully understand the vertical structure of the near FFT interface region. To estimate the suspended solids concentration (CV ) over the entire water column, a laboratory calibration of the turbidity sensors is performed and the linear relationship CV [mg=L] = 0.84 x Turb [NTU] is obtained. This corresponds to concentrations of approximately 200mg=L for the region located just above the peak of turbidity, at the bottom of BML. The point of zero turbidity corresponding to the upper limit of the sensors is estimated at approximately 40 g=L. This value must be considered as a minimum solids concentration for the region located below the peak of turbidity. A small optical device is built using a waterproof camera in order to validate the previous results by applying another method than turbidity. The values obtained are comparable and this visually-based estimation can be useful to better understand turbidity variations. Convective cooling, which is one of the processes possibly affecting the bottom turbid layer during fall turnover, is studied in the laboratory on a kaolinite suspension. A simplified experiment using the melting of an ice cube to generate surface cooling shows the rapid rise of the turbid layer as cold water penetrates across its interface. This results in a decrease of bottom turbidity and an increase of mid-depth turbidity. The convective process is then roughly modelled using plume theory and conservation equations. The results obtained are in the same order of magnitude than the values observed. A more realistic experiment with a more uniform and gradual cooling of the water surface suggests that convective cooling might affect the bottom turbid layer by eroding its interface and slowly entraining particles to the water above.

In an environment subject to anthropogenic pressures, the understanding of lakes is crucial as they are essential for ecosystems and represent a source of the scarce accessible freshwater existing on Earth. Water quality management is especially designed to protect this precious resource and relies on monitoring programs and model simulations. Case study of this project, Greifensee is a small eutrophic lake located in the northern plateau of Switzerland (ZH). For decades, it has been subject to nutrient-­‐rich runoff from agricultural activities in its catchments, consequence of the fast population growth in the area. These considerable human-­‐related pressures have led to a strong process of eutrophication and significantly altered its water quality. In recent years, although nutrient inputs have been reduced, the lake has still not fully recovered and remains classified as eutrophic. This project developed a 3D coupled hydrodynamic-­‐biological model for Greifensee using the software Delft-­‐3D from Deltares in the Netherlands. Delft-­‐3D has been widely applied in various situations and validated, which makes it an excellent tool for such project. Moreover, the development of the model also relies on two monitoring campaigns, from the Eawag institute and Zürich Kanton. Finally, while the model provides an almost full spatio-­‐temporal representation of the processes happening in this lake, final results simulated fairly well the general trends of chlorophyll-­‐a, dissolved oxygen, orthophosphate and ammonium in terms of mass content and depth distribution. Understanding the ecological dynamics of a eutrophic lake using such kind of simulation will hopefully contribute, on a longer-­‐term perspective, to the better management of the lake towards the recovery of its former ecological status.

Remote-sensing of water surfaces such as large lakes is a useful tool for monitoring and understanding large-scale processes. Suspended particles in lakes can have various sources such as autochthonously produced organic matter, urban or agricultural runoff or rivers inflows. Understanding their sources and impacts on natural waters is highly important as they are the mirror of the ecological well being. As suspended solids can be retrieved by remote-sensing based on their reflectances, satellite images are an important tool to study the lake and detecting important processes and events. Before using the reflectances measured by the sensor for monitoring lakes, atmospheric corrections have to be applied on the image for retrieving accurate data. This project compares three different algorithms for atmospheric corrections, namely Acolite developed in Belgium, OPERA developed at Vito and C2RCC designed by Brockmann Consulting, applied on the case study, the Lake of Geneva. The resulting reflectances from the different algorithm settings are compared to the in-situ water-leaving reflectance measurements. Additionally, the total suspended matter concentrations derived from the output reflectances were validated with in-situ concentrations. C2RCC with elevation indication performs a good atmospheric correction and yield good particulate concentrations by non-ideal atmospheric conditions. Acolite with a linear parameter of 9.5 gives good results by perfect weather conditions. This projects depicts guidelines and recommendations for performing atmospheric corrections over the Lake Geneva with these algorithms.

Bathymetry is a crucial variable for many researches, such as monitoring of the coral ecosystems. Traditional bathymetric measurements are made by echo-sounder, a type of sonar, measuring water depth from sea surface. Nevertheless, this acquisition process remains expensive and cannot be applied everywhere. Despite less accurate results, passive satellite derived bathymetry can provide a large-scale resolution at a lower cost. This study explores the potential of empirical models applied on images provided by Sentinel-2 sensor for bathymetry retrieval. Technical issues and suitable conditions are described here. In addition, a different approach is proposed. It is composed of an initial step designed to classify areas relying on their bottom reflectance and their water optical properties. Tests are achieved in New Caledonia, in the South West part of the lagoon. The method showed its ability to produce bathymetric data at a large scale, including shallow coral areas, which are difficult to measure by boat. The proposed approach allowed to improve the results of traditional empirical models. For this reason, satellite derived bathymetry can provide a valuable alternative for researchers needing to study coral ecosystems.

Lake mesoscale processes have no secrets for artists, they have some for scientists and policy-makers. In the introduction to this dissertation, we saw that poets and painters depict the lake with rich variability. This vision conflicts with conventional approaches inferring the lake's bio-physical status from a few in-situ measurements with limited spatio-temporal coverage. Yet it reflects upon true physical processes, capable of disrupting the misleading lentic nature of lakes, the essential ecosystem services they provide, and even citizens' safety. Recent overarching policies now aim at securing those services, using novel approaches like numerical simulations and remote sensing observations. Harnessing the potentiality of in-situ, remote sensing data and model simulations, this thesis developed an end-to-end framework delivering reliable synoptic lake information, at high spatial and temporal resolution. In lakes, three-dimensional hydrodynamic models are the only information source capable of resolving transport and mixing, and forecasting their dynamics. However, they still rely on large observational datasets for their complex parameterizations and for constraining their uncertainties. This thesis addressed such challenges by (i) implementing an automated model calibration framework alleviating the need for expert knowledge, and by (ii) developing a data assimilative scheme capable of reducing and quantifying model uncertainties by incorporating satellite and in-situ data. Both yielded remarkable results: the former returned parametric values diminishing models Root Mean Square Error by up to 47 %, while the latter cut it further down by 54 %. Furthermore, the data assimilation enhanced the spatial coherence and magnitude of imperfectly resolved physical processes, and provided system uncertainties. Finally, this thesis delivered a practical outcome of its findings by developing an online pre-operational three-dimensional lake monitoring and forecasting system: meteolakes.ch. For two years, Meteolakes has been disseminating spatially explicit real-time lake information and data products to more than hundred thousand end-users. This pioneering platform has been featured in numerous media (newspapers, radio, television), public events, museum exhibitions, and benefited scientific, lake professionals, and public communities. A pinnacle of this research has been its early-warning and forecasting capabilities, which anticipated numerous mesoscale physical phenomena in Lake Geneva, such as upwellings, gyres, and strong currents. Two of those events, which impacted public and commercial activities, are illustrated in this dissertation. From observations and models to societal benefit, we created here a long value chain for water management. At the crossroads of scientific, computational and observational advances, this research paves the route for understanding lakes' delicate imbalance. By producing data society can use, it opens novel frontiers for interdisciplinary research on previously elusive lake physical processes, and their implications on the everyday life of people.

Dams store water and trap sediment in their reservoirs. Downstream river segments, hence, are affected by a limited sediment dynamics. This becomes obvious by river bed incision, limited geomorphological variability and depletion of hydraulic habitats for in-stream ecological organisms. Replenishment is a measure to counteract the lack of sediment. In segments dams such a sediment replenishment can be combined with the release of an artificial flood, by activating spillways and bottom outlets. Recent laboratory studies revealed the potential of multi-deposit replenishment configuration towards an increase of geomorphological richness in the river. However, this has not yet been tested in the field. The hydro-morphological index of diversity (HMID), is based on the spatial variability flow depth and velocity in a river segment, allowing the quantification of the change in morphology such a measure. Its ease in computation and its objectivity makes the index a useful tool for a large variety of users. However, knowledge concerning data sufficiency and a standardized sampling procedure does not exist. Further, the HMID does not account for temporal variability. This research aims at closing these gaps of knowledge for a sustainable management of complex floodplains downstream of dams. Flow depth and velocity data from 19 river segments were analyzed with the HMID. Structured sub-sampling and analysis of the data revealed different data sufficiency depending on the complexity of the river geomorphology. A representative HMID value is computed from at least 100 datapoints distributed over eight cross-sections, in braided rivers more datapoints are required. The geomorphological changes by an artificial flood event in the Sarine were analyzed with the HMID. In the impact perimeter of the multi-deposit sediment replenishment, the HMID increased by 36 % in the Sarine, in the rest of the river 18 %. A similar study was investigated at the Spöl, pointing out that sediment availability is crucial for the hydraulic habitat diversity. With the help of 489 tracer stones, the movement of the replenished sediment was investigated in detail. The deposition pattern results in repeating sediment clusters on the riverbed, as it was observed in the laboratory experiments. For the two characteristic diameters, the tracers allowed the estimation of transport velocities of 19 cm/min (dm = 57 mm) and 28 cm/min (d90 = 113 mm) during the flood event and consequently the erosion efficiency of the different parts of the flood hydrograph. Macroinvertebrates were less affected by the artificial flood event in the hydropeaking river segment of the Sarine compared with the residual flow segment. The species diversity indices decreased significantly due to the artificial flood event. A direct link between flow regime and EPT richness was observed. A river with a natural flow regime hosts the highest richness of macroinvertebrates followed the residual and finally the hydropeaking flow regime. For other ecological indicators, additional physical river parameters for example the frequency duration curve or the grain size distribution need to be considered as well.

In many countries water quality is a major concern for drinking water management authorities. Freshwater is a limited resource and the demand for good-quality water from natural aquatic systems is therefore high. Additional stress arises from anthropogenic emissions of nutrients, chemicals, pathogens, heat and hydrological alterations as well as from the ongoing global climate change. In this thesis the relevant recent past, present and future factors affecting water quality in the perialpine Lake Biel, used as a source for drinking water, was investigated. Through measurements in the field combined with hydrodynamic logical modelling in one and three dimensions, optimal locations for forthcoming lake water intakes was identified. Water quality properties considered were temperature, oxygen, suspended sediment concentration (SSC) and the risk of subaqueous mass movements. The results identified the forthcoming changes expected in Lake Biel due to the upcoming decommission of the Mühleberg Nuclear Power Plant (MNPP) in 2019. This plant currently release ~700 MW of heat into the upstream Aare River in the form of cooling water. The removal of this anthropogenic thermal source will decrease future lake temperature by ~0.3 °C (volume average). Due to seasonal river discharge patterns, the main impact of the plant closure will occur during winter. Minor effects are expected in summer in the form of moderately weaker lake stratification. Furthermore, the current fate of thermal pollution emitted from MNPP was linked to the hydraulic residence time of Lake Biel. While short-term anthropogenic thermal impacts in Lake Biel can be large, the system is additionally experiencing continuous warming up to ~0.1 °C per decade (volume average) by the ongoing climate change. The climate effect on Lake Biel and its primary tributary, the Aare River, was investigated as well as compared to the much larger Lake Geneva and Rhône River. Climate change causes seasonal river discharge shifts resulting in enhanced river warming in summer and diminished warming in winter, while at the same time SSC increases in winter and decreases in summer. Differences in temperature as well as warming rates between rivers and lakes in turn resulted in a discharge and hydraulic residence time-dependent decrease in climate warming of lakes. Furthermore, deep-water renewal in both lakes is predicted to increase in summer and decreases in winter, possibly influencing the replenishment of deep water oxygen. Additionally, sedimentation patterns in Lake Biel were examined and linked to the historical diversion of the Aare River into the lake. The majority of sediment supplied to Lake Biel (~80 %) came from large SSC events in the Aare. These events resulted in a selective particle settling pattern, which concentrated sedimentation on the shallow shelf area North-East of the Aare delta. Both the large SSC events as well as this selective sedimentation pattern were connected to weather fronts coming in from the Atlantic Ocean. The research performed here opens up for further promising interdisciplinary research between Meteorology, Climatology, Hydrology and Sedimentology. Inland water management would benefit through increased knowledge regarding the propagation of particles and/or anthropogenic heat, from river catchments into downstream lakes and sediments.

In this study, a hydrodynamical model is coupled to a biogeochemical model, and then used to simulate the main physical, chemical and biological characteristics of Lake Geneva. The study period, going from 1981 to 2016 was marked by two major changes with concomitant effects: re-oligotrophication by reducing the phosphorus loading and climate change. Thanks to the calibrated model, changes of the ecosystem related to climate change and re-oligotrophication were disentangled. It resulted in a positive effect of the former on phytoplankton biomass and primary production, and a negative effect of the latter. The combined effects of these two majors changes are negative. However, these results have a large uncertainty related to the capacity of the model to reproduce the biological characters of Lake Geneva. The calibration procedure must be improved to ensure a higher relevance of the results.