River and open-channel flows are free surface boundary layer flows with complex 3D, large-scale, turbulent structures. The study of 2D and 3D large-scale turbulent flow structures is a great challenge for physicists, mathematicians and engineers from such different domains as civil, environmental and mechanic engineering. Different processes can generate 3D, large-scale, turbulent structures which occur at the same time. On the one hand, large scale vortical structures such as secondary currents of Prandtl's second kind play an important role in the understanding of 3D turbulent structures in straight channels and rivers. Secondary currents affect bottom shear stress and longitudinal mean velocity, and contribute to sediment transport and air-water gas exchange by creating upwelling and downwelling motion in the water column. At the free surface, such upwelling and downwelling motion is an important mechanism for the air-water gas exchange and is considered to be responsible for surface boils. On the other hand, experimental work in turbulent boundary layers revealed the existence of bursting resulting in hairpin shaped structures which are responsible for the link between the inner and the outer layer. The interaction between these two layers in turbulent boundary layers is considered in terms of the dynamics of momentum, energy, and Reynolds shear stress transport. In order to advance in the understanding of this fundamental problem in turbulent open-channel flow, recently developed measurement and observation techniques are used in this Ph.D study. A non-intrusive Acoustic Doppler Velocity Profiler (ADVP), Surface Large Scale Particle Image Velocimetry (LSPIV) and a hot-film probe were combined in the investigation of coherent structures, secondary currents, surface boils and their interaction in turbulent rough-bed open-channel flow. The ADVP permits to measure 3D quasi-instantaneous velocity profiles in the entire water depth and to investigate the mean field and the fluctuating field of all three velocity components. The LSPIV system, developed at the LHE, allows visualizing the water surface and obtaining the surface velocity information in relation to instantaneous surface vortical structures. Bottom shear stress was measured with a sensor based on the hot film principle. The instruments provided the mean and instantaneous velocity field in the entire water depth and at the free surface. Six sets of experiments were carried out in turbulent rough bed open-channel for three different width-to-depth ratios (12.25, 15 and 20) at high, moderate and low Reynolds numbers. The results of the ADVP measurements show mean longitudinal velocity patterns undulating across the channel which indicate patterns of secondary currents in the mean flow structure. Upwelling regions can be identified by lower relative mean longitudinal velocities close to the free surface, and downwelling regions can be identified by higher relative mean longitudinal velocities. It is observed that the existence of secondary currents affects the distribution of bed shear stress and Reynolds stress across the channel. Bed shear stress show a cross-channel undulation pattern with bed shear stress in downwelling areas being higher than in upwelling areas. The Reynolds shear stress distribution in the water column has revealed the same undulating pattern. The number of secondary flow cells is determined by the aspect ratio and relative roughness. It is found that the bottom roughness elements of the channel bed make these longitudinal cells stable. The Reynolds number does not affect the spanwise position of the upwelling and downwelling regions of the secondary cells, but it does affect and slightly increase the normalized Reynolds shear stress. Secondary currents with cells whose dimensions are equal to the flow depth are the most stable and dominant pattern. Changes in the vorticity pattern causes changes in turbulence characteristics in upwelling and downwelling regions. Our study and existing investigations demonstrated that one of the most probable mechanisms for the initiation of multi cellular secondary currents is the mutual interaction between the rough bed and the pre-existing secondary currents near the side wall. The occurrence of small and large scale coherent structures, such as hairpin packets, and their relation to secondary currents are investigated through a quantitative analysis of instantaneous flow fields over the entire turbulent boundary layer across the channel. Uniform momentum zones are clearly detected in the instantaneous velocity fields in the longitudinal direction. In the logarithmic layer, the coherent vortex packets originating from the wall layer frequently occur within larger moving zones of uniform momentum, and extend up to the middle of the boundary layer. Good results in terms of dimension and position of large coherent structures relating to zones of uniform streamwise momentum support the concept of a dynamic link of hairpin packets and zonal organization in the outer layer. Secondary currents are large-scale streamwise vortical structures that affect the organization of coherent structures in the outer layer. More hairpin vortex packets could be carried by upwelling, with positive vertical velocity increasing the height of Zone 2. In the downwelling region, the height of Zone 2 and the growth angle of the hairpin packets decrease compared to the upwelling region, because of the negative vertical mean velocity of the secondary currents. This may prevent hairpin vortex packets from reaching the free surface due to the higher gradient of the longitudinal velocity. A quadrant analysis in the upwelling and downwelling regions revealed that in the wall region of downwelling areas, sweep events are dominant, and in the region close to the free surface, ejection events dominate over sweep events. The dominance of ejection events at the free surface explains the occurrence of a large number of surface boils observed in the upwelling regions. The measurements have shown that secondary currents and coherent structures are correlated, thus producing 3D flow structures. The results from LSPIV show a mean multi-cellular pattern of faster and slower primary longitudinal surface velocities. Streaks of faster longitudinal velocity are found in downwelling areas. Upwelling areas are identified with lower velocities. In addition, we observed mean transversal surface currents between upwelling and downwelling zones. We have shown that near the surface, ejections which are part of the large scale burst cycle are more common in upwelling zones between secondary current cells. Measurements reveal that these vortex boils mainly occur in upwelling areas with high vorticity, whereas downwelling areas show lower vorticity. Up- and downwelling zones, as well as surface boils are observed at all Reynolds numbers and aspect ratios. Therefore, they can be considered important processes in river dynamics and affect transport between the surface and the pelagic zone. Based on the combined results from LSPIV, ADVP and hot-film data, this study experimentally demonstrated that secondary currents, surface boils and coherent structures are correlated and produce 3D flow structures. The effect of secondary currents on tracer distribution in open-channel and river flow is to disperse and mix tracers in three dimensions more rapidly than would be the case if turbulent diffusion were acting alone. This has important consequences for pollutant spreading. Together with surface boil vortices, these currents contribute to surface renewal and gas transfer. In downwelling zones, the water masses moved along the surface by the transversal currents are transported downwards faster than by turbulent mixing. Again, the dispersion and mixing due to secondary currents discussed above will then provide for rapid 3D distribution in the entire water column. This thesis is a contribution to understanding of the transport and mixing dynamics in open-channel flow with an emphasis on the effects of coherent structures, secondary currents and surface boils, as well as the interaction between them. The information which was obtained advances the understanding of fine and large scale dynamics in open-channel flow. At the same time it contributes to the improvement of algorithms in numerical predictive water quality models, which in turn improve effective water resources management.