Située à l'interface entre les eaux de surface et les eaux souterraines, la zone hyporhéique (ZH) est depuis maintenant plusieurs décennies considérée comme une zone cruciale pour la préservation des milieux aquatiques. Elle constitue souvent un indicateur fiable de la bonne qualité des eaux et une niche écologique primordiale pour de nombreuses espèces. Mais elle est aussi le lieu d'interaction entre deux masses d'eau de signature différente, ce qui conduit à la formation d'un milieu extrêmement fragile et siège d'un grand nombre de réactions biogéochimiques. L'objectif principal de cette thèse est de parvenir à une meilleure compréhension de la dynamique des échanges au sein de la zone hyporhéique. L'approche de cette problématique s'est faite sous un aspect innovant en couplant une démarche hydrogéologique "classique" à l'aide de mesures hydrodynamiques et géochimiques, et l'utilisation de la tomographie de résistivité électrique (ERT). Plusieurs campagnes de terrain ont été menées sur la rivière Essonne, choisie comme lieu d'expérimentation. Différents outils de prélèvement et/ou de mesure ont été mis en place et un grand nombre de mesures à différentes périodes de l'année ont été réalisées. Des expériences assez techniques et innovantes de suivi d'un abaissement et relèvement de barrage, ainsi qu'un traçage artificiel au sel ont pu être effectués grâce à la collaboration avec le syndicat chargé de la gestion et l'aménagement d'une partie du réseau hydrographique de l'Essonne (SIARCE). En parallèle avec cette étude expérimentale, une maquette numérique 3D de la zone d'étude a été réalisée à l'aide du logiciel HydroGeoSphere. Des tests de sensibilité ont permis d'identifier les paramètres hydrodynamiques les plus importants et de quantifier leur impact sur la formation et l'évolution de la zone hyporhéique. Finalement, les premières simulations des expériences menées sur le terrain ont permis de confronter l'approche expérimentale et l'approche théorique. / The Hyporheic Zone (HZ) is located at the interface between surface water and groundwater. For several decades it is considered as a hotspot for the development of a rich aquatic environment in rivers. Its system is often considered as a reliable indicator for water quality and a primary ecological niche for many species. From a hydrological point of view, it is also the place of interaction between two distinct water bodies with different geochemical signatures. This place of mixing forms a very fragile equilibrium where many biogeochemical reactions can occur. The objective of this thesis is to reach a better understanding of mixing and water fluxes in a dynamic context within the hyporheic zone. An innovative method was used by coupling a "classic" hydrogeological approach with hydrodynamic and geochemical measurements with Electrical Resistivity Tomography (ERT). Several field campaigns were done on the Essonne river as experimental site. A large number of measurements were done at various periods of the year and field equipment for water sampling and measurements were installed during these three years. Technical and innovative experiments were conducted such as a dam lowering and rising and an artificial salt tracer test in collaboration with the federation in charge of organization and management of the Essonne network. Finally, a 3D-model of the studied area was built with the HydroGeosphere software. The main hydrodynamic parameters have been tested in order to understand their impact and their variation in a static or dynamic environment on the hyporheic system and its development. In addition, field experiments were reproduced to compare the experimental and theoretical approach.

<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>

Hydroelectric releases on the Deerfield River in northwestern Massachusetts affect surface water-groundwater interactions there by daily reversing the head gradient between river and groundwater. Artificially elevated stage drives river water into the riparian aquifer. Water budget analysis indicates that roughly 10% of this bank-stored water is permanently lost from the river system in a 19.5 km reach, likely as a result of transpiration by bank vegetation. Field observations as well as two-dimensional modeling results show that water losses are not uniform throughout the study reach. Riparian aquifer transmissivity in river sub-reaches largely determines the magnitude of surface water-groundwater exchange as well as net water loss from the river. These newly documented dam-induced losses from river systems inform decisions by river managers and hydroelectric operators of additional tradeoffs of oscillatory dam-release river management.

Streams and rivers have been modified in the past centuries for agricultural purposes. The Baltic Sea suffers from problems regarding eutrophication. Regulations of point-sources have decreased nutrient levels, but for a scattered source of nutrient pollution, streams are important. One way of mitigating nitrogen is with coupled denitrification and nitrification processes when stream water is transported through flow paths in the hyporheic zone, an area in the stream sediments where groundwater and stream water mix. Tullstorps brook is an agricultural stream that flows into the Baltic Sea. It has had problems with high nutrient loads and poor water quality and has therefore been restored. The fieldwork in this project was conducted in Tullstorps brook in May 2019, where Rhodamine WT (RWT) tracer test and Hydraulic Conductivity (HC) measurements were done in 3 reaches, and compared to similar fieldwork since before restorations, during the summer of 2015. Two reaches in an agricultural setting that have been restored, Reach 4 and Reach 6, were measured, as well as a control reach, Reach 5, which is in a natural setting. The tracer tests indicated a significant decrease in the velocity in remediated reaches. The results of exchange velocity between the stream flow and the hyporheic zone suggest an increase after remediation of the reaches and the residence time seems to be decreasing simultaneously. When comparing the hydraulic characteristics, different stream flow during measurements was considered in a qualitative manner. The results of HC measurements show a decrease from 2015 to 2019 in the remediated reaches. In Reach 4 it decreased from 1.20E-03 m/s to 5.0E-4 m/s and in Reach 6, HC decreased from 7.70E-04 m/s before remediations to 5.6E-04 m/s after remediation actions. All the measurements have uncertainties, especially since homogeneity is assumed to some extent and the natural environment will always be heterogeneous.

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The hyporheic zone is the reactive interface between surface water and groundwater found beneath streams and rivers, where chemical gradients and an abundant biological presence allow beneficial attenuation of contaminants. Such attenuation often requires reactants from surface water and groundwater to mix, but few studies have explored the controls on mixing of upwelling groundwater water in the hyporheic zone and its potential to foster mixing-dependent reactions. The goals of this dissertation are therefore to evaluate the effects of (1) hydraulic controls and (2) reaction kinetic controls on hyporheic mixing and mixing-dependent reactions, and (3) use two-dimensional visualization techniques to quantify patterns of hyporheic mixing and mixing-dependent reactions. These objectives were addressed by hyporheic zone simulations using a laboratory sediment mesocosm and numerical models. In the laboratory, a hyporheic flow cell was created to observe both conservative dye mixing and abiotic mixing-dependent reaction. The numerical models MODFLOW and SEAM3D were then used to simulate the experimental data to better understand hydraulic and transport processes underlying laboratory observations and provide sensitivity analysis on hydraulic and reaction kinetic parameters. Visualization techniques showed a distinct mixing zone developing over time for both conservative and reactive conditions. Mixing zone thickness in both conditions depended on surface water head drop and the ratio of boundary inflows of surface water and groundwater (inflow ratios). The abiotic reaction caused the mixing zone to shift even under steady-state hydraulics indicating that hyporheic zone mixing-dependent reactions affect the location of mixing as chemical transformations take place. The numerical model further showed the production zone to be thicker than the mixing zone and located where reactants had already been depleted. Finally, mapping of two-dimensional microbial respiration (i.e., electron acceptor utilization) patterns in streambed sediments using dissolved oxygen and carbon dioxide planar optodes showed that coupling multiple such 2D chemical profiles can enhance understanding of microbial processes in the hyporheic zone. Temporal dynamics for these chemical species revealed development of spatial heterogeneity in microbial respiration and hence microbial activity. Our results show key hydrologic and biogeochemical controls on hyporheic mixing and mixing-dependent reactions. These reactions represent a last opportunity for attenuation of groundwater borne contaminants prior to entering surface water. / Doctor of Philosophy / The boundary between surface water and groundwater beneath streams and rivers is known to have an abundant biological presence that allows for beneficial reduction of contaminants when chemicals combine. This combination of chemicals due to mixing of the waters is an important characteristic of the boundary area (defined as the hyporheic zone). However, controls on mixing and the impact on contaminant reduction are not fully understood. Therefore, the goals of this dissertation are to evaluate (1) the effects of varying water level and flow and (2) the effects of the rates of the reaction on mixing of chemicals and chemical transformation, and (3) use two-dimensional visualization processes to quantify the reactions and mixing occurring at the boundary area of surface water and groundwater. We used both laboratory and numerical model simulations to study mixing at the boundary area. The two-dimensional visualization in both laboratory and numerical models show distinct regions where mixing occurred between the surface water and groundwater. The extent of the mixing (mixing thickness) was most dependent on the flow ratio between the upward groundwater and downward surface water. The observations were made with non-varying surface and groundwater flow rates but changes on the mixing thickness and location were seen throughout the duration of the experiments revealing that chemical reaction dynamics have an influence on the mixing process. Ultimately, these types of reactions represent a last opportunity for attenuation of groundwater borne contaminants prior to entering surface water.

A principal ecological role proposed for the hyporheic zone is as a refugium that promotes benthic invertebrate survival during adverse conditions in the surface stream. Whilst a growing body of work has examined use of this hyporheic refugium during hydrological extremes (spates, streambed drying), little research has considered variation in refugium use over prolonged periods including contrasting conditions of surface flow. In this thesis, benthic invertebrate use of the hyporheic refugium is considered at monthly intervals over a five-month period of variable surface flow, at nine sites in two groundwater-dominated streams, the River Lathkill (Derbyshire) and the River Glen (Lincolnshire). Conditions identified as potential triggers of refugium use included a flow recession and a high-magnitude spate on the Lathkill, and small spates and a decline in flow preceding localised streambed drying on the Glen. During flow recession, reductions in submerged habitat availability and concurrent increases in benthic population densities were dependent on channel morphology. An unusual paired benthic-hyporheic sampling strategy allowed the type of refugium use (active migration, passive inhabitation) to be inferred from changes in hyporheic abundance and the hyporheic proportion of the total population. Using this approach, evidence of active migrations into the hyporheic zone use was restricted to two instances: firstly, Gammarus pulex (Amphipoda: Crustacea) migrated in response to habitat contraction and increased benthic population densities; secondly, migrations of Simuliidae (Diptera) were associated with low-magnitude spates. Refugium use was site-specific, with refugial potential being highest at sites with downwelling water and coarse sediments. A conceptual model describing this spatial variability in the refugial capacity of the hyporheic zone is developed for low flow conditions. In some cases, hyporheic refugium use was apparently prevented by disturbance-related factors (rapid onset, high magnitude) regardless of the refugial potential of the sediments. The extension of the hyporheic zone's refugial role to include low flows highlights the need to explicitly protect the integrity of hydrologic exchange in river rehabilitation schemes. However, the limited capacity of the hyporheic refugium emphasizes the additional importance of maintaining habitat heterogeneity including multiple instream refugia.

The hyporheic interstitial was recognized as an integral zone within the aquatic ecosystem bearing important functions for both adjacent compartments, surface and ground water, about 50 years ago. Since then, rather disciplinary works gained knowledge on the organismic community of this ecotone, its spatial extent, the role of distinct parameters such as hydrology and morphology, temporal characteristics, process dynamics, the role for stream or groundwater quality and restoration measures. However, a systematic study on the risks to the hyporheic functions was missing to date. This thesis combined existing methods in order to gather an integrated set of information allowing for the assessment of the ecotonal status. This approach was applied to investigate the functional behavior towards stressors like increasing nutrient and fine sediment input into a rather pristine environment. An interdisciplinary risk assessment and the establishment of adapted measures was called for as land-use scenarios for the studied catchment area indicated progressive onland erosion. Therefore firstly, an integrated monitoring scheme was drawn up and conducted at three sites along a river that underlay a stressor gradient such as mentioned before. Secondly, the data sets were analysed in order to evaluate the status of the hyporheic funtions at the riffles. Thirdly, a coupled surface-subsurface modelling approach was set up to further study the impact of the stressors on the ecotonal integrity. And fourthly, an interdisciplinary consideration combined with studies on the catchments sediment budget and the rivers ecological status was applied to identify measures for the restoration and protection of the aquatic ecosystem. The analysis of the data gathered with the help of the established monitoring scheme revealed that elevated nutrient or fine sediment input lead to biological or physical clogging, respectively, with consequences for the hyporheic zone functions. The surface - ground water connectivity was either lowered in summer months, when biofilm growth was highest, or permanently, as fine sediment particles infiltrated into the interstices of the riverbed sediment. Scouring did not seem to take place as high amounts of fine particles were found in the matrix after discharge events of snowmelt and summer precipitation. With respect to the biogeochemical regulation function, biofilm material appeared to provide an autochthonous carbon source boosting microbial substance turnover. The sediment underneath the physical clogged layer was cut off from carbon and oxygen rich surface water and thus was not reactive. However, the enhanced surface area provided by the fine sediment within the topmost sediment layer seemed to support microbial processing. The inclusion of the results of a study concerning the ecological status at the investigated reaches lead to the deduction that biological clogging at the present degree was not affecting habitat quality. Whereas the physical clogging had tremendeous and lasting effects on the macroinvertebrate community which carries to the conclusion that sediment management within the studied catchment is of uttermost importance. A scenario analysis reflecting distinct clogging degrees and types with a calibrated model of a studied riffle within a pristine reach proved the observed loss of hydrologic connectivity due to physical and biological clogging. Further, a treshold of oxygen consumption rates above which the reproduction of salmonid fish would be unsuccessful was identified for the settings of the middle reaches. In summer month with low discharge it seemed to be likely that this treshold might be reached. Following, a dynamic discharge may be decisive to protect the ecotonal integrity. The integration with the outcome of an investigation regarding the sediment sources within the catchment allowed for two suggestions. On the one hand, river bank restoration and protection within the middle reaches need to be prioritised, and on the other hand, the conservation of the natural vegetation at the steep slopes within the mountaineous areas need to be undertaken in order to secure the pristine aquatic environment of this area. Hyporheic zone research of the last decade was driven by testing hypotheses on the functional significance of distinct spatial and temporal configurations in the field and by new modelling approaches. However, data on the quantification of the ecological impact of clogging processes were lacking. The thesis contributed to the systemic understanding of the hyporheic zone being affected by physical and biological clogging and new field data within a degrading pristine environment were generated, accessible for further hyporheic research. The interdisciplinarity enabled comprehensive statements for the usage of an Integrated Water Resources Management plan.

A physical assessment of the Provo River Restoration Project was undertaken in order to determine how alterations to the channel were designed, the nature of as-built channel morphology, and the performance of the reconfigured channel in terms of achieving frequent (2-year recurrence) bankfull discharge and increasing transient storage. Measures of channelized and reconfigured channel morphology were obtained using total station survey, digital aerial photography, and pebble counts. Results of geomorphic analysis were compared with similar measurements made by a regional consulting company, and stream channel design data, in order to determine that intended mitigation included reducing channel capacity, increasing sinuosity, decreasing pool spacing, and decreasing the size of bed material. Reconfiguration of the channel resulted in somewhat enlarged cross-sections with reduced mean velocities, increased sinuosity, decreased pool spacing, and decreased bed substrate size. One-dimensional hydraulic modeling suggests that alterations to channel morphology have increased the bankfull channel capacity in most reaches. Modeling results illustrate the fact that the stage of the 2-year recurrence flood is below bankfull at most cross-sections. This result does not follow the intentions of channel design. However, we have observed floodplain inundation in most years since reconfiguration. The occurrence floodplain inundation is being facilitated by overbank flow at a few point locations illustrating the strengths of incorporating variability into design. Known geomorphic controls on transient storage were reconfigured in manner to potentially increase in-channel and hyporheic components of transient storage. Stream tracer tests were utilized in order to determine the degree to which these alterations affected transient storage. Numerical analysis of stream tracer tests suggests that while the relative area of transient storage increased, average residence time of water in storage, and the mass transfer rate of solute between storage and the stream did not change. This suggests that an extensive hyporheic zone may not have been established. Correlations between hydrologic and geomorphic parameters indicate that in-stream storage may have been increased, and quick-exchange hyporheic flowpaths may have been created. (295 pages)