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.