This thesis was motivated by the need to advance the knowledge on the variability and dynamics of energy fluxes in lakes and reservoirs, as well as about the physical processes that regulate the fluxes at both the air and water side of the air-water interface. In the first part, I re-examine how mechanical energy, resulting from its major source – the vertical wind energy flux - distributes into the various types of water motions, including turbulent flows and surface and internal waves. Although only a small fraction of the wind energy flux from the atmosphere is transferred to the water, it is crucial for physical, biogeochemical and ecological processes in lentic ecosystems. Based on extensive air- and water-side measurements collected at two small water bodies (< 10 km2), we estimated the energy fluxes and energy content in surface and in internal waves. Overall, the estimated energy fluxes and energy content agree well with results reported for larger water bodies, suggesting that the energetics driving the water motions in enclosed basins is similar, independently of the basin size. Our findings highlight the importance of the surface waves that receive the largest fraction of the wind energy flux, which strongly nonlinearly increases for wind speeds exceeding 3 m s-1. We found that the existing parameterization of the wave height as a function of wind speed and fetch length did not reproduce the measured wave amplitude in lakes. On average, the highest energy content was observed in basin-scale internal waves, together with high-frequency internal waves exhibiting seasonal variability and varies among the aquatic systems. During our analysis, we discovered the diurnal variability of the energy dissipation rates in the studied lake, suggesting biogenic turbulence generation, which appears to be a widespread phenomenon in lakes and reservoirs. In the second part of the thesis, I addressed current knowledge gaps related to the bulk transfer coefficients (also known as the drag coefficient, the Stanton number and the Dalton number), which are of a particular importance for the bulk estimation of the surface turbulent fluxes of momentum, sensible and latent heat in the atmospheric boundary layer. Their inaccurate representation may lead to significant errors in flux estimates, affecting, for example, the weather and climate predictions or estimations of the near-surface current velocities in lake hydrodynamic models. Although the bulk transfer coefficients have been extensively studied over the past several decades (mainly in marine and large-lake environments), there has been no systematic analysis of measurements obtained at lakes of different size. A significant increase of the transfer coefficients at low wind speeds (< 3 m s-1) has been observed in several studies, but, to date, it has remained unexplained. We evaluated the bulk transfer coefficients using flux measurements from 31 lakes and reservoirs. The estimates were generally within the range reported in previous studies for large lakes and oceans. All transfer coefficients increased substantially at low wind speeds, which was found to be associated with the presence of gusts and capillary waves (except the Dalton number). We found that the Stanton number is systematically higher than the Dalton number. This challenges the assumption made in the Bowen-ratio method, which is widely used for estimating evaporation rates from micrometeorological measurements. We found that the variability of the transfer coefficients among the lakes could be associated with lake surface area. In flux parameterizations at lake surfaces, it is recommended to consider variations in the drag coefficient and the Stanton number due to wind gustiness and capillary wave roughness while the Dalton number could be considered as constant at all wind speeds. In the third part of the thesis, I address the key drivers of the near-surface turbulence that control the gas exchange in a large regulated river. As all inland waters, rivers are an important natural source of greenhouse gases. The effects of the widespread alteration and regulation of river flow for human demands on gas exchange is largely unknown. In particular, the near-surface turbulence in regulated rivers has been rarely measured and its drivers have not been identified. While in lakes and reservoirs, near-surface turbulence is mainly related to atmospheric forcing, in shallow rivers and streams it is generated by bottom friction of the gravity-forced flow. The studied large regulated river represents a transition between these two cases. Atmospheric forcing and gravity were the dominant drivers of the near-surface turbulence for a similar fraction of the measurement period. Based on validated scalings, we derived a simple model for estimating the relative contributions of wind and bottom friction to near-surface turbulence in lotic ecosystems with different flow depths. Large diel variability in the near-surface energy dissipation rates due to flow regulation leads to the same variability in gas exchange. This suggests that estimates of gas fluxes from rivers are biased by measurements performed predominantly during daytime. In addition, the novelty in all the analyses described above is the use of the turbulent surface fluxes measured directly by the eddy-covariance technique – at the moment of writing, the most advanced method. Overall, this thesis is of a potential interest for a broad range of scientific disciplines, including limnology, micrometeorology and open channel hydraulics.

The work presented in this thesis investigated interactions of selected biophysical processes that affect zooplankton ecology at smaller scales. In this endeavour, the extent of changes in swimming behaviour and fluid disturbances produced by swimming Daphnia in response to changing physical environments were quantified. In the first research question addressed within this context, size and energetics of hydrodynamic trails produced by Daphnia swimming in non-stratified still waters were characterized and quantified as a function of organisms’ size and their swimming patterns. The results revealed that neither size nor the swimming pattern of Daphnia affects the width of induced trails or dissipation rates. Nevertheless, as the size and swimming velocity of the organisms increased, trail volume increased in proportional to the cubic power of Reynolds number, and the biggest trail volume was about 500 times the body volume of the largest daphnids. Larger spatial extent of fluid perturbation and prolonged period to decay caused by bigger trail volumes would play a significant role in zooplankton ecology, e.g. increasing the risk of predation. The study also found that increased trail volume brought about significantly enhanced total dissipated power at higher Reynolds number, and the magnitudes of total dissipated power observed varied in the range of (1.3-10)X10-9 W. Furthermore, this study provided strong evidence that swimming speed of Daphnia and total dissipated power in Daphnia trails exceeded those of some other selected zooplankton species. In recognizing turbulence as an intrinsic environmental perturbation in aquatic habitats, this thesis also examined the response of Daphnia to a range of turbulence flows, which correspond to turbu-lence levels that zooplankton generally encounter in their habitats. Results indicated that within the range of turbulent intensities to which the Daphnia are likely to be exposed in their natural habitats, increasing turbulence compelled the organisms to enhance their swimming activity and swim-ming speed. However, as the turbulence increased to extremely high values (10-4 m2s-3), Daphnia began to withdraw from their active swimming behaviour. Findings of this work also demonstrated that the threshold level of turbulence at which animals start to alleviate from largely active swimming is about 10-6 m2s-3. The study further illustrated that during the intermediate range of turbu-lence; 10-7 - 10-6 m2s-3, kinetic energy dissipation rates in the vicinity of the organisms is consistently one order of magnitude higher than that of the background turbulent flow. Swarming, a common conspicuous behavioural trait observed in many zooplankton species, is considered to play a significant role in defining freshwater ecology of their habitats from food exploitation, mate encountering to avoiding predators through hydrodynamic flow structures produced by them, therefore, this thesis also investigated implications of Daphnia swarms at varied abundance & swarm densities on their swimming kinematics and induced flow field. The results showed that Daphnia aggregated in swarms with swarm densities of (1.1-2.3)x103 L-1, which exceeded the abundance densities by two orders of magnitude (i.e. 1.7 - 6.7 L-1). The estimated swarm volume decreased from 52 cm3 to 6.5 cm3, and the mean neighbouring distance dropped from 9.9 to 6.4 body lengths. The findings of this work also showed that mean swimming trajectories were primarily horizontal concentric circles around the light source. Mean flow speeds found to be one order of magnitude lower than the corresponding swimming speeds of Daphnia. Furthermore, this study provided evidences that the flow fields produced by swarming Daphnia differed considerably between unidirectional vortex swarming and bidirectional swimming at low and high abundances respectively.

Sediment transport contributes to the movement of inorganic and organic material in rivers. The construction of a dam interrupts the continuity of this sediment transport through rivers, causing sediments to accumulate within the reservoir. Reservoirs can also act as carbon sinks and methane can be released when organic matter in the sediment is degraded under anoxic conditions. Reservoir sedimentation poses a great threat to the sustainability of reservoirs worldwide, and can emit the potent greenhouse gas methane into the atmosphere. Sediment management measures to rehabilitate silted reservoirs are required to achieve both better water quantity and quality, as well as to mitigate greenhouse gas emissions. This thesis aims at the improvement of sediment sampling techniques to characterize sediment deposits as a basis for accurate and efficient water jet dredging and to monitor the dredging efficiency by measuring the sediment concentration. To achieve this, we investigated freeze coring as a method to sample (gas-bearing) sediment in situ. The freeze cores from three reservoirs obtained were scanned using a non-destructive X-Ray CT scan technique. This allows the determination of sediment stratification and character-ization of gas bubbles to quantify methane emissions and serve as a basis for the identi-fication of specific (i.e. contaminated) sediment layers to be dredged. The results demon-strate the capability of freeze coring as a method for the characterization of (gas-bearing) sediment and overcomes certain limitations of commonly used gravity cores. Even though the core’s structure showed coring disturbances related to the freezing process, the general core integrity seems to not have been disturbed. For dredging purposes, we analyzed the impact pressure distribution and spray pattern of submerged cavitating wa-ter jets and determined the effects of impinging distances and angles, pump pressures and spray angles. We used an adapted Pressure Measurement Sensing technique to enhance the spatial distribution, which proved to be a comparatively easy-to-use meas-urement method for an improved understanding of the governing factors on the erosional capacity of cavitating water jets. Based on this data, the multiple linear regression model can be used to predict the impact pressure distribution of those water jets to achieve higher dredging accuracy and efficiency. To determine the dredging operational efficien-cy, we developed a semi-continuous automated measurement device to measure the sediment concentration of the slurry. This simple and robust device has lower costs, compared to traditional and surrogate sediment concentration measurement technolo-gies, and can be monitored and controlled remotely under a wide range of concentrations and grain-sizes, unaffected by entrained gas bubbles

Change of ecosystems and the associated loss of biodiversity is among the most important environmental issues. Climate change, pollution, and impoundments are considered as major drivers of biodiversity loss. Organism traits are an appealing tool for the assessment of these three stressors, due to their ability to provide mechanistic links between organism responses and stressors, and consistency over wide geographical areas. Additionally, traits such as feeding habits influence organismal performance and ecosystem processes. Although the response of traits of specific taxonomic groups to stressors is known, little is known about the response of traits of different taxonomic groups to stressors. Additionally, little is known about the effects of small impoundments on stream ecosystem processes, such as leaf litter decomposition, and food webs. After briefly introducing the theoretical background and objectives of the studies, this thesis begins by synthesizing the responses of traits of different taxonomic groups to climate change and pollution. Based on 558 peer-reviewed studies, the uniformity (i.e., convergence) in trait response across taxonomic groups was evaluated through meta-analysis (Chapter 2). Convergence was primarily limited to traits related to tolerance. In Chapter 3, the hypothesis that small impoundments would modify leaf litter decomposition rates at the sites located within the vicinity of impoundments, by altering habitat variables and invertebrate functional feeding groups (FFGs) (i.e., shredders), was tested. Leaf litter decomposition rates were significantly reduced at the study sites located immediately upstream (IU) of impoundments, and were significantly related to the abundance of invertebrate shredders. In Chapter 4, the invertebrate FFGs were used to evaluate the effect of small impoundments on stream ecosystem attributes. The results showed that heterotrophic production was significantly reduced at the sites IU. With regard to food webs, the contribution of methane gas derived carbon to the biomass of chironomid larvae was evaluated through correlation of stable carbon isotope values of chironomid larvae and methane gas concentrations. The results indicated that the contribution of methane gas derived carbon into stream benthic food web is low. In conclusion, traits are a useful tool in detecting ecological responses to stressors across taxonomic groups, and the effects of small impoundments on stream ecological integrity and food web are limited.

The physical-biological interactions that affect the temporal variability of benthic oxygen fluxes were investigated to gain improved understanding of the factors that control these processes. This study, for the first time is able to resolve benthic diffusive boundary layer (DBL) dynamics using the newly developed lifetime-based laser induced fluorescence (τLIF) oxygen imaging system, which enables study of the role of small-scale fluid mechanics generated by benthic organism activity, and hence a more detailed analysis of oxygen transport mechanisms across the sediment-water interface (SWI). The net benthic oxygen flux across the sediment-water interface is controlled by sediment oxygen uptake and oxygen transport. While the oxygen transport is largely influenced by turbulence driven by large-scale flows, sediment oxygen uptake is mainly affected by oxygen production and biological- and chemical-oxygen degradation of organic matter. Both processes can be enhanced by the presence of fauna and are intimately coupled. The benthic oxygen flux can be influenced by fauna in two ways, i.e. by modulating the availability of oxygen, which enhances the sediment oxygen uptake, and by enhancing the transport of oxygen. In-situ and a series of laboratory measurements were conducted to estimate the short- and seasonal variability of benthic fluxes including the effects of burrow ventilation activity by tube-dwelling animals using eddy correlation (EC) and τLIF oxygen imaging techniques, respectively. The in-situ benthic oxygen fluxes showed high variability at hourly and seasonal timescales, where statistical analysis indicated that current velocity and water depth were the most significant predictors of benthic oxygen flux at the waterside, which co-varied with the discharge, temperature, and oxygen concentration. The range of variability of seasonal fluxes corresponded to the friction velocities which were driven by large-scale flows. Application of a simplified analytical model that couples the effect of hydrodynamic forcing of the diffusive boundary layer with a temperature-dependent oxygen consumption rate within the sediment showed that friction velocity and temperature cause similar variability of the steady-state benthic oxygen flux. The application of τLIF oxygen imaging system in bioturbation experiments enabled the investigation and discovery of insights into oxygen transport mechanisms across the sediment-water interface. Distinct oxygen structures above burrow openings were revealed, these were associated with burrow ventilation. The DBL was degraded in the presence of burrow ventilation. Advective transport generated by the energetic plumes released at burrow outlets was the dominant transport driving mechanism. The contribution of diffusive flux to the total estimated decreased with increasing larval density. For a range of larvae densities, commonly observed in ponds and lakes, sediment oxygen uptake rates increased up to 2.5-fold in the presence of tube-dwelling animals, and the oxygen transport rate exceeded chironomid respiration by up to a factor of 4. The coupled physical-biological factors affecting net benthic oxygen flux can be represented by temperature, which is a prominent factor that accounts for both oxygen transport and sediment oxygen uptake. Low oxygen transport by flow coincided with high summer temperatures, amplified by a reduction of benthic population density and pupation. It can also, however, be offset by increased ventilation activity. In contrast, low temperature coincided with high oxygen concentrations, an abundance of larvae, and higher flow is offset by less burrow ventilation activity. Investigation of the effect of hydrodynamics on oxygen transport alone suggested that the expected increase of benthic oxygen flux under global warming can be offset by a reduction in flow velocity, which could ultimately lead to increasing carbon burial rates, and in a growing importance of anaerobic mineralization pathways with increasing emission rates of methane. This study suggests a significant contribution of biological induced benthic oxygen flux to physical transport driven by large-scale flow-fields contributing to bottom-boundary layer turbulence.