The deployment of in-stream flow-energy converters in rivers is an opportunity to expand the renewable energy portfolio and limit carbon emissions. Device performance and lifetime, environmental conservation, and the safety of fluvial communities against flood events, however, present unresolved challenges. In particular, we need to understand how multiple submerged hydrokinetic turbines interact with the sediment bed and whether existing technologies can be deployed in morphodynamically active natural rivers. Here, we present a scaled demonstration of a hydrokinetic turbine power plant deployed in a quasi-field-scale channel with sediment transport and migrating bedforms. We measure high-frequency sediment flux, the spatiotemporally resolved bathymetry and the turbine model performance. We find that with opportune siting, kinetic energy can be extracted efficiently without compromising the geomorphic equilibrium of the river and the structural safety of the turbine foundation, even in the presence of large migrating dunes, thus paving the way for harnessing sustainable and renewable energy in rivers.