Marine and Hydrokinetic (MHK) energy is an emerging renewable and sustainable technology which harnesses kinetic energy of natural water flows such as tides, rivers and ocean currents. In particular, rivers are currently an overlooked source of local and continuous kinetic energy that can be exploited using the available in-stream converters technology. The uncertainties regarding the interaction between these devices and the surrounding environment complicate the regulatory permitting processes, slowing down the expansion of MHK industry. A crucial issue that needs further attention is the interaction between these devices and the physical fluvial environment such as the bathymetry, sediment transport, and the associated morphodynamic processes. Analytical and experimental research conducted at Saint Anthony Falls Laboratory (SAFL) addressed this topic, unveiling the local and non-local (far from the device location) effects of hydrokinetic turbines on channel bathymetry and morphology. A theoretical model framework based on the phenomenology of turbulence was derived to predict the scour at the base of MHK device. Asymmetric installations of turbine array models within multi-scale laboratory channels were observed to trigger river instabilities known as forced-bars. Results suggest that the amplitude of these instabilities might be reduced by limiting the power plant lateral obstruction within the channel cross-section. A 12-turbine staggered array also proved to be resilient to intense flooding conditions, encouraging the expansion of this technology to large sandy rivers. Current research is investigating how hydrokinetic technology can be synergistically integrated in rivers, not only minimizing the environmental costs but also providing a positive feedback on the channel. Experiments suggest that turbines strategically installed in the river (i.e. at the side bank in yawed condition or in a vane-shaped array) could be used as stream bank protection systems and, eventually, be integrated in stream restoration projects.