As recently shown in laboratory bench scale experiments, chemotaxis, i.e.the movement of microorganisms toward or away from the concentration gradient of a chemical species, could have a fundamental role in the transport of bacteria through saturated porous media. Chemotactic bacteria could enhance bioremediation by directing their own motions to residual contaminants in less conductive zones in aquifers. The aim of the present work is to develop a proper numerical scheme to define and to quantify the magnitude and the role of chemotaxis in the complex groundwater system framework. We present a new class of meshless Lagrangian particle methods based on the Smooth Particle Hydrodinamics (SPH) formulation of Vila & Ben Moussa, combined with a new Weighted Essentially Non-Oscillatory (WENO) reconstruction technique on moving point clouds in multiple space dimensions. The purpose of this new scheme is to fully exploit the advantages of SPH among traditional meshbased and meshfree schemes and to overcome its inapplicability for modeling chemotaxis in porous media. The key idea is to produce for each particle first a set of high order accurate Moving Least Squares (MLS) reconstructions on a set of different reconstruction stencils. Then, these reconstructions are combined with each other using a nonlinear WENO technique in order to capture at the same time discontinuities and to maintain accuracy and low numerical dissipation in smooth regions. The numerical fluxes between interacting particles are subsequently evaluated using this MLS-WENO reconstruction at the midpoint between two particles, in combination with a Riemann solver that provides the necessary stabilization of the scheme based on the underlying physics of the governing equations. We propose the use of two different Riemann solvers: the Rusanov flux and an Osher-type flux. The use of monotone fluxes together with a WENO reconstruction ensures accuracy, stability, robustness and an essentially non oscillatory solution without the artificial viscosity term usually employed in conventional SPH schemes. To our knowledge, this is the first time that the WENO method, which has originally been developed for mesh-based schemes in the Eulerian framework on fixed grids, is extended to meshfree Lagrangian particle methods like SPH in multiple space dimensions. In the first part, we test the new algorithm on two dimensional blast wave problems and on the classical one-dimensional Sod shock tube problem for the Euler equations of compressible gas dynamics. We obtain a good agreement with the exact or numerical reference solution in all cases and an improved accuracy and robustness compared to existing standard SPH schemes. In the second part, the new SPH scheme is applied to advection-diffusion equation in heterogeneous porous media with anisotropic diffusion tensor. Several numerical test case shows that the new scheme is accurate. Unlike standard SPH, it reduces the occurrence of negative concentration. In the third part, we show the applicability of the new scheme for modeling chemotaxis in porous media. We test the new scheme against analytical reference solutions. Under the assumption of complete mixing at the Darcy scale, we perform different two-dimensional conservative solute transport simulations under steady-state conditions with instant injection showing that chemotaxis significantly affect the quantification of field-scale mixing processes.

Fine-grained sediment represents a significant component of the total transport load in most fluvial systems around the world that are not limited to the alluvial rivers with sandy beds. A variety of natural or human actions, such as fire, logging, flow diversion, road construction, and urban or agricultural development can increase the supply of sand to a gravel- and cobble-bedded rivers. From hydrodynamics point of view, if the coarsest part of the sediments mixture composing the bed grain size composition cannot be transported, a coarser immobile layer can develop through vertical sorting of grain size fraction. This layer has influence on the grain size transport rate describes qualitatively as a competition between absolute and relative grain size effects. The absolute size effect causes the inherent mobility of sediment grains to decrease with increasing grain size. The relative size effect tends to increase the transport rate of larger grains and decrease the transport rate of smaller grains, characterizing the supply-limitation conditions for the fine fraction of the bed composition. Two-fraction approximation (i.e. sand and gravel/cobble fraction) of widely sorted sediment might capture mixed-size transport dynamics of practical significance is suggested by a number of observations, because the fines content of the bed fs may often be more variable than that of the coarse fraction (i.e. partial mobility condition), and whose passage, intrusion, or removal may be a specific environmental or engineering objective. The problem of sand transport over gravel bed has been addressed in several recent field and laboratory studies. Bed load transport rate and suspension entrainment rate are related, among other, to the sand elevation hs in the gravel framework, because the parameter hs not only controls the amount of volume of sand available to be transported by the flow, but also affects the relative sand coverage with respect to the gravel rough elements. To this regard, experimental studies showed that the function hs controls the geometrical transition from gravel framework (i.e. fs < 0.1 - 0.2) to sand matrix with interbedded gravel clasts (i.e. fs > 0.3 - 0.4), depending on the diameter ratio of sand and gravel fraction. Moreover, sand elevation hs is also a measure of the sediment supply-limitation that, in its turns, controls the sand bedform development. A limited volume of bedload sediment leads either to smaller dimensions, the sediment starved bedform or fewer isolated bedforms. Bedform types that are typically associated with partial mobility condition are: sand ribbons, barchanoid dunes, isolated dunes and sediment starved dunes, bedload sheets and low-relif bedforms. The state of knowledge suggests that there has been relatively little attention paid to understand physically which are the hydrodynamics mechanisms that control the sand transport in a gravel bed. The relevance of the present work is mainly in offering a mechanistic tool that can be used to better understand which physical phenomena control the development of sand bedforms when sand is transported over an immobile gravel bed, specifically the present research aims to: - understand physically how the local sand surface elevation hs affects the characteristic spatial scales of the bed with sand level-dependent roughness; - understand physically how the local sand surface elevation hs influences the transport phenomenon of the sand fraction when the gavel framework is at rest; - integrate the analysis of already published work often with different specific goal compared to that stated above; - determine the hydraulics conditions that controls the sand dunes formation when the sand bed elevation hs varies in the gravel framework. On the basis of the above main objectives, the present research propose a conceptual morphodynamic model accounting for the key processes of sand transport over a gravel matrix, taking into account near-bed conditions locally adapted to the evolving sand surface patterns relative to the turbulent near-bed characteristics and to the transport characteristics of fines.

Freshwater ecosystems are severely undergoing degradation due to the presence of multiple stressors that are undermining their biodiversity. In this sense, quantifying these effects on Alpine regions is challenging, due to the lack of tailored field measurements of hydrological, biological and chemical variables. This work aims to touch some of these aspects, with particular attention to hydrological dynamics and their effects on macroinvertebrates. Field activities have been conducted within the Adige catchment which has been selected as a case study in the FP7 project GLOBAQUA. Collected data have been analyzed by means of statistical tools and results showed a seasonal and spatial variability of biological communities related to hydrological and chemical variables. In particular, it has been observed that richness, diversity and relative composition of macroinvertebrates community are chiefly affected by hydrological alteration and urban pollution. Available literature confirmed that hydrological alteration is one of the most important factors affecting riverine ecosystems. In Alpine regions, most of the hydrological alterations observed are due to hydropower that represents the major source of energy in the Trentino-Alto Adige region. Since the introduction of the free energy market in Italy, hydropower production shows large fluctuations at the daily and larger temporal scales, as the managers aim at producing when the energy price is high. This increased the variability of streamflow downstream the restitution of the power plants. Changing climate is an additional stressor that can enhance the effects of these anthropogenic influences. Thereby, in this work hydrological alterations have been distinguished between those forced by climate change and those caused by the presence of hydropower plants and have been analysed in detail. The former have been analysed downstream of the Careser glacier, which has long-term observations of climatic variables, mass balances and streamflow. The main purpose of this study was finding a direct relationship linking biological indicators to streamflow variations related mainly to hydropower operations. Quantifying these effects is challenging due to the fact that the behaviour by which macroinvertebrates respond remains largely unexplained. However, analyses of similarities and independence, performed at the basin scale with data provided by the local Environmental Protection Agencies, showed evident differences in the biological communities between impacted and non-impacted sites. These results bring us to believe that a relationship between biological data and hydrological alteration is expected to exist, but that is not clearly explicated by simple correlations. Giving a quantitative interpretation of this correlation could help hydropower manager to improve and optimize the energy production with a more realistic scenario of the effects on the biological community, with also a perspective of the combined effects caused by the presence of multiple reservoirs within the basin.

The water-energy nexus holds paramount relevance in the context of the transition to a carbon free energy system, being water the only renewable energy source with reliable storage capacity. Modelling hydropower production in a large domain over a long time window represents an open challenge due to a variety of reasons: firstly, high-resolution, large-scale hydrological modelling in a context of uncertainty needs calibration, thus representing a computationally intensive task due to the large domain and time window over which calibration is needed; secondly, as stated by many works in literature, hydropower production modelling and in particular reservoir modelling is a very information-demanding procedure, and excessive simplifications adopted to face the lack of information might lead to consistent bias in the predictions. This thesis can be subdivided into three main parts: firstly, the model that was used to perform every analysis, HYPERstreamHS, will be presented. The model is a continuous, large-scale hydrological model embedding a dual-layer MPI framework (i.e. Message Passing Interface, a common standard in parallel computing) that ensures optimal scalability of the model, greatly reducing the computation time needed. Explicit simulation of water diversions due to hydropower production is also included in the model, and adopts only publicly available information, making the model widely applicable. Secondly, a first validation of the model will be presented, and the adopted approach will be compared with some other approaches commonly found in literature, showing that the inclusion of a high level of detail is crucial to ensure a reliable performance of the model; this first application was performed on the Adige catchment, where extensive information on human systems was available, and allowed to effectively assess which information were indispensable and which, in turn, could be simplified to some extent while preserving model performance. Finally, the model setup has been applied on a relevant portion of the Western Italian Alps; in this case, two different meteorological input forcing data sets were adopted, in order to assess the differences in their performance in terms of hydropower production modelling. This latter study indeed represents a preliminary analysis and will provide stepping stone to extend the modelling framework to the Italian Alpine Region.

This research tries to fill a gap between two very different scales of enquiry: the local (i.e. hillslope) scale, where detailed investigations are possible but difficult to generalize over large areas, and the landscape (i.e., catchment) scale, where representation of the physics is minimised, the resolution in space and time is maximised, and the focus is upon predicting emergent properties rather than system details. Specifically, this Thesis focused on an aspect of the geosciences that is of critical current concern: the representation of the interface between hydrological response and geomorphic processes, notable mass movements. At present there remains a great difficulty at this interface: detailed geotechnical and hydrological studies of mass movements reveal exceptionally complex interlinkages between water and the surface sediment mass, notably dynamically at the onset and during mass release; but these kinds of studies are only possible with a very detailed description of the three-dimensional structure of the porous media and its hydrological and mechanical response during (and after) rainfall events. Such analyses are feasible but tend to result in analyses that are restricted in terms of geographical generalisation. On the other hand, approaches that apply to larger spatial scales tend to over-simplify the representation of critical failure processes, such as in the assumptions that infinite slope stability analysis can be applied to failures that are finite in their slope length, or that upslope contributing area can always act as a surrogate for the hydrologic response at a point in the watershed. The innovative element in this research lies on the assessment of rainfall-induced shallow landslide occurrence over large spatial scales, whilst accepting that shallow landslides triggering may be influenced by processes that operate over much smaller scales. Specifically, this Thesis focuses upon connection by subsurface flow pathways. New model approaches that incorporate connectivity are required to address the findings of field hydrologists. Thus, this Thesis starts from the understanding of small-scale hydrological processes to develop a large-scale topographic index-based shallow landslide model that includes the concept of subsurface hydrological connectivity. The research aims to provide a tool for more realistic assessments of when shallow landslides may occur and where landsliding may occur at the catchment scale to support decision makers in developing more accurate land-use maps and landslide hazard mitigation plans and procedures.

Il presente lavoro di tesi è strutturato in tre sezioni principali. La prima, che comprende i primi due capitoli, riguarda i riferimenti per la conoscenza: al fine di definire il contesto mondiale nel quale si inserisce la tesi, vengono analizzati i dati riguardanti i disastri naturali avvenuti e quelli relativi ai possibili scenari futuri anche in relazione ai cambiamenti climatici. La seconda parte, dedicata ad approfondimenti alle scale europea e italiana, effettua nei capitoli 3-4-5 una sorta di downscaling dei primi due: la medesima struttura di analisi viene riproposta, applicata e approfondita ad una scala spaziale di maggior dettaglio, prima quella europea e successivamente quella nazionale, focalizzando l’attenzione su un particolare tipo di disastro, vale a dire le alluvioni. La terza sezione concretizza il contributo metodologico del lavoro proponendo una nuova metodologia per l’elaborazione dei piani di protezione civile comunali o intercomunali, in particolare in riferimento agli scenari di rischio idraulico, e la sua diffusione con relativa verifica applicativa. / The present study is composed of three main sections. The first, covering the first two chapters, deals with references to knowledge: in order to define the worldwide scenario to which this study is referred, data on really occurred natural disaster and on possible future events are analyzed, considering also the probable influence of the on-going climate changes. The second part, chapters 3-4-5, is a sort of downscaling to the European and Italian territory of the first two chapters’ analysis. The same methodology is detailed and implemented for the analysis of a particular event’s type: flood risk (in Europe and Italy). Third section is about the methodological contribution of the study: a new approach to civil protection planning at local level is suggested, with a particular focus on flood risk scenarios. This new civil protection planning methodology has been applied to a real context and the relative case study is presented.

After the seminal works by Freeze and Harlan (1969), the scientific community realized that groundwater and vadose zone equation were breaking up. Hydrologists split into three communities following the motto “you are my boundary condition”: groundwater people, vadose zone scientists and surface water hydrologists. This compartmentalization of the scientific community fostered a deepening of knowledge in single branches, allowing to break things down into simple parts. However, this division represented an obstacle to the comprehension of the complexity that characterises the interactions between them. Eventually, this separation of the communities continued into software code. As a matter of fact, the boundary conditions were hard-wired, but they offered a poor representation of the physics in the interaction between different domains. Recently, there has been a renewed interest in studying the big picture, the interactions between different domains. This it is evident in the development of a new research field named the Earth’s Critical Zone (CZ). It is defined as the “ heterogeneous, near surface environment in which complex interactions involving rock, soil, water, air, and living organism regulate the natural habitat and determine the availability of life-sustaining resources” (National Research Council, 2001). Further interest in the studying the CZ is given by the ever-increasing pressure due to the growth in human population, wealth, and climatic changes. This thesis focuses on the CZ while recognising the central role of having a solid set of tools for modeling the water movements in all conditions. Recently, Prentice et al. (2015) identified Reliable, Robust, and Realistic, the three R’s, as the three characteristics that numerical models should have. Soil moisture is one of the key components to simulate the processes in the critical zone. The governing equation to describe the water flow in a porous material is know as the Richards equation and it dates back to 1931.The numerical solution of the Richards equation is far from trivial because of its mildly nonlinearity and it is often discarded in favour of more empirical models. After the pioneering work by Celia et al. (1990), a lot of work has been done in this direction and several model, for instance Hydrus, GEOtop, Cathy, Parflow adopted variants of the Newton algorithm to allows global convergence. Since Casulli and Zanolli (2010), anticipated by Brugnano and Casulli (2008), a new method called nested Newton has been found to guarantee convergence in any situation, even under the use of large time steps and grid sizes. The research presented in this thesis used this integration algorithm. Besides the numerical aspect, another issue was the correct definition of the boundary condition at the soil surface. As a matter of fact, the definition of the surface boundary condition is necessary to capture the generation of surface run-off. In the literature several approaches were proposed to couple surface and subsurface flow, and in this work the approach presented by Gugole (2016) has been used. The novelty regarded the discretization of the shallow water equation and the Richards equation in an unique algebraic system that was solved in a conservative manner. Richards equation was criticized from many points of view, but it is difficult to criticize its core mass conservation. The definition of the hydraulic properties of the soil, including both the soil water retention function (SWRC) and the hydraulic conductivity models, often uses simplified representation of the pore system describing it as bundle of cylindrical capillaries where the largest ones drain first and are filled last. As pointed out by Bachmann et al. (2002), “physical effects, like surface water film adsorption, capillary condensation and surface flow in liquid films, as well as volumetric changes of the pore space are often ignored”. Thus, the capillary bundle concept is a rough, even if still useful approximation of soil reality. From these observations, during the research the code has been designed to offer the opportunity to easily implement new soil water hydraulic models that might be proposed in the future. The Richards’ equation alone is not anymore sufficient to model the water flow in soils. In fact, soil temperature affects the water flow in soils. This is evident in cold regions where soil water is subject to freezing and thawing processes, but also in unfrozen soil, where temperature modifies water properties such as viscosity, the surface tension, and the contact angle. These microscopic variations of the water physical properties have significant impacts in the mass and energy budget within the CZ. For instance, it has been observed that the infiltration rates between the stream and the vadose zone show a clear diurnal pattern: infiltration rates are highest in late afternoon, when stream temperature is greatest, and they are lowest in early morning when stream temperature is least. In cold regions the run-off production is strongly affected by the presence of ice with the soil. Nonetheless, soil moisture modifies the thermal properties of the soil: water is characterised by a high thermal inertia and the thermal conductivity of ice is almost four times larger than that of liquid water, and water flow carries a significant amount of sensible heat. These aspects come under one the R of realistic. Hence, the Richards’ equation has been coupled with the energy equation for the unfrozen case. Moreover, the research developed a model to study the heat transfer considering the phase change of water. In both cases robust numerical schemes have been used. There are few models that already coupled the equations. One of these models is GEOtop that was conceived and built in the research group where this work was carried out. Such models have some limitations. One of the main limitations regards their implementations. In fact, these models were built as a monolithic code and this turns in difficulties in maintaining and developing existing codes. In this work the codes have been developed by using Design Patterns. As a result, the codes are easy to maintain, to extend, and to reuse. Considering the CZ, these aspects are of crucial importance. Researchers should have a model that can be extended to include more processes, i.e. increase its complexity and avoiding the code to become too complicated. The models were integrated in the Object Modelling System v3 (OMS3) framework. The system provides various components for precipitation treatment, radiation estimation in complex terrain, evaporation and transpiration that can be connected to each other’s for generating inputs and outputs. Due to the modularity of the system, whilst the components were developed and can be enhanced independently, they can be seamlessly used at run time by connecting them with the OMS3 DSL language based on Groovy. OMS3 provides the basic services and, among them, tools for calibration and implicit parallelization of component runs. In sum, the thesis analyses the relevant literature to date. It presents a detailed description of the physical processes related to the water flow and the energy budget within the soil. Then, it describes the numerical method used to solve and coupled the equations. It also provides the informatics behind WHETGEO 1D (Water HEat Tracers in GEOframe). Finally, the work focuses on the WHETGEO extension for the bidimensional case by showing how the code can be designed to store grid information.

In the Veneto Città Diffusa, the decentralized urban landscape of the Veneto Region, Northeast Italy, the economic growth of recent decades brought about increased urbanization and agricultural intensification. The process of change has been accompanied by the extension and/or maximization of centralized services of drinking water, irrigation, waste water and drainage to meet greater demands for the provision and disposal of water. Accordingly, the structure of a formerly poor rural landscape has been adapted to support an affluent industrialized and urban one. However, all this has had detrimental side effects, which, in time might seriously compromise the quality of life in this landscape. On one side, the transformations that occurred have in fact given rise to unexpected problems of drought, flooding and pollution of water; and recent changes in climate patterns have further intensified these risks. On the other side, the long term fine grained carrying structures of the landscape fabric –like roads, field ditches, stream and river corridors, dirt roads, paths etc.-, as the very basis of the landscapeâ€TMs unique ecological diversity, and once used to convey the areaâ€TMs flows now risk general extinction. The existing road system is also increasingly under pressure to intensify traffic that creates congestion, pollution and unsafe conditions. From a planning and design perspective, this calls for adequate methods and tools that can help designers to tackle the needs for more sustainable water flows as well as the needs for a recovered ecological integrity (including spatial intelligibility) of this urban landscape. This can be of a great importance also for a better understanding of other territories of urban dispersion which are spreading especially over the European and –although in very different forms- the American continents. The present research aims to contribute to the planning and design answers to these urgent problems. For this purpose, the urban landscape of the Veneto Città Diffusa was approached with principles derived from an Integrated Water Management approach (IWM) that, recently, has been successfully applied in the urban context as an alternative to the technocratic approach of maximizing flows. Storage of water is the key principle, for it can bring about decentralized storage, which means new and different water flow management and spatial arrangements. This can ultimately be obtained through the placement and implementation of small scale and decentralized infrastructures. By focusing on the interrelation between flow patterns and spatial arrangements in a small portion of the Veneto Città Diffusa –i.e. the case study landscape- the study has elaborated and confirmed two specific closely related assumptions. The first assumption is that the recent loss of landscape diversity and the increasing problems of flood, drought and water pollution of the Veneto Città Diffusa are closely related and ascribable also to the processes of centralization of the water flows that accompanied the areaâ€TMs economic growth. The changes of flow patterns and spatial arrangements of the case study area that happened over the last decades were systematically observed in a threefold area-flow-actor perspective. Insights into the present arrangements of irrigation, drainage, drinking water and waste water at the scale of the Consorzio di Bonifica Valli Grandi e Medio Veronese waterboard also accompanied the investigation. The diagnosis showed that the centralized systems arranged to perform greater inflows and outflows, draw heavily on resources and often risk exceeding the regionâ€TMs ecological carrying capacity. Moreover, the centralized arrangement often conflicts with the decentralized character of the settlements. No synergetic relations have been developed between the man-made water system and the existing pervasive fine grained elements of the landscape. Instead, this rich capital asset has been left behind and even neglected. And such forms of negligence have ultimately brought about a massive loss of biodiversity, accessibility and spatial intelligibility of the local landscape. This leads to the second assumption that has been researched: in the decentralized urban landscape of the Veneto Città Diffusa, answers that design measures can give in response to increasing water-flow dysfunctions and loss of diversity can be based on decentralized water storage systems that make use of the existing fine grain structures of local landscapes –ditches, streams, land depressions, former pits, hedge-rows, dirt roads, paths etc.- and promote a local-based utilisation of resources (resilience), while fostering a stronger local identity, biodiversity and accessibility for more coherent spatial arrangements. Building on the Ecological Conditions Strategy conceived by Tjallingii (1996), a set of guiding models was developed. In the models, the principles of Integrated Water Management were tuned to those fine grained landscape elements that still structure the low plains of the Veneto –the built lot system, the agricultural field system, the road system, the stream system and the excavation site system. Principles and models of integration and decentralization drove the exploration of design options for different levels of decentralized management of water in the case study area. The creative design process of learning produced a useful toolbox of design models. The design exploration also proved that the dispersed urbanization of the Città Diffusa can be made suitable to accommodate modern integrated and decentralized water systems that, by re-activating the existing carrying structures, also contribute to recovering the landscape. Decentralized urbanization can actually be an ally in the search for sustainable and legible settlements that also reuse and recycle water locally. Designing an integrated water system that fits with the Città Diffusa and contributes to the ecological integrity of this urban landscape remains an important challenge. The tools that can be of practical help to designers and decision-makers who are willing to undertake this challenge were investigated and worked out. Nonetheless, the way to realize the outlined strategies is complex and affected by uncertainty. In this context more research is needed to investigate the effects of decentralization at the level of the region on one side, and on the other side to investigate how these integrated systems can be set to fit present institutional and market frameworks. In conclusion, the study generated concrete proposals for one or more pilot projects that will be extremely important to creating consensus in the decision process during the testing of models and strategies.

Hydrogeological hazards are quite diffuse rainfall-induced phenomena that affect mountain regions and can severely impact these territories, producing damages and sometimes casualties. For this reason, hydrogeological risk reduction is crucial. Mitigation strategies aim to reduce hydrogeological risk to an acceptable level and can be classified into structural and non-structural measures. This work focuses on enhancing some non-structural risk mitigation measures for mountain areas: debris-flow rainfall thresholds, as a part of an Early Warning System (EWS), multivariate rainfall scenarios with multi-hazard mapping purpose and public awareness. Regarding debris-flow rainfall thresholds, an innovative calibration method, a suitable uncertainty analysis and a proper validation process are developed. The Backward Dynamical Approach (BDA), a physical-based calibration method, is introduced and a threshold is obtained for a study area. The BDA robustness is then tested by assessing the uncertainty in the threshold estimate. Finally, the calibrated threshold's reliability and its possible forecast use are assessed using a proper validation process. The findings set the stage for using the BDA approach to calibrate debris-flow rainfall thresholds usable in operational EWS. Regarding hazard mapping, a multivariate statistical model is developed to construct multivariate rainfall scenarios with a multi-hazards mapping purpose. A confluence between a debris-flow-prone creek and a flood-prone river is considered. The multivariate statistical model is built by combining the Simplified Metastatistical Extreme Value approach and a copula approach. The obtained rainfall scenarios are promising to be used to build multi-hazard maps. Finally, the public awareness within the LIFE FRANCA (Flood Risk ANticipation and Communication in the Alps) European project is briefly considered. The project action considered in this work focuses on training and communication activities aimed at providing a multidisciplinary view of hydrogeological risk through the holding of courses and seminars.

The need to consider groundwater and surface water as a single resource has fostered the interest of the scientific community on the interactions between surface water and groundwater. The region below and alongside rivers where surface hydrology and subsurface hydrology concur is the hyporheic zone. This is the region where water exchange determines many biogeochemical and ecological processes of great impact on the functioning of rivers. However, the complex processes taking place in the hyporheic zone require a multidisciplinary approach. The combination of innovative point and distributed techniques originally developed in separated disciplines is of great advantage for the indirect identification of water exchange in the hyporheic zone. Distributed techniques using temperature as a tracer such as fiber-optic distributed temperature sensing can identify the different components of groundwater-surface water interactions based on their spatial and temporal thermal patterns at the sediment-water interface. In particular, groundwater, interflow discharge and local hyporheic exchange flows can be differentiated based on the distinct size, duration and sign of the temperature anomalies. The scale range and resolution of fiber-optic distributed temperature sensing are well complemented by geophysics providing subsurface structures with a similar resolution and scale. Thus, the use of fiber-optic distributed temperature sensing to trace flux patterns supported by the exploration of subsurface structures with geophysics enables spatial and temporal investigation of groundwater-surface water interactions with an unprecedented level of accuracy and resolution. In contrast to the aforementioned methods that can be used for pattern identification at the interface, other methods such as point techniques are required to quantify hyporheic exchange fluxes. In the present PhD thesis, point methods based on hydraulic gradients and thermal profiles are used to quantify hyporheic exchange flows. However, both methods are one-dimensional methods and assume that only vertical flow occurs while the reality is much more complex. The study evaluates the accuracy of the available methods and the factors that impact their reliability. The applied methods allow not only to quantify hyporheic exchange flows but they are also the basis for an interpretation of the sediment layering in the hyporheic zone. For upscaling of the previous results three-dimensional modelling of flow and heat transport in the hyporheic zone combines pattern identification and quantification of fluxes into a single framework. Modelling can evaluate the influence of factors governing groundwater-surface water interactions as well as assess the impact of multiple aspects of model design and calibration of high impact on the reliability of the simulations. But more importantly, this modelling approach enables accurate estimation of water exchange at any location of the domain with unparalleled resolution. Despite the challenges in 3D modelling of the hyporheic zone and in the integration of point and distributed data in models, the benefits should encourage the hyporheic community to adopt an integrative approach comprising from the measurement to the upscaling of hyporheic processes.