In-stream hydrokinetic energy conversion devices can be deployed in large scale rivers to produce energy with minimal infrastructure costs. They are however shown to actively interact with the channel bathymetry and sediment transport generating a scour and deposition pattern similar to bridge pier. Symmetric, streamwise, aligned turbine installations have shown to introduce only local effects, yet complex configurations may trigger non-local morphodynamic instabilities. Experimental investigations, based on continuous spatio-temporal measurements of bed topography, explore a number of inflow conditions and siting strategies for axial-flow hydrokinetic turbine models. Results show that asymmetric turbine installations in a portion of the channel cross section may introduce weak non-local deformation of the mean bed topography and alter bedform migration velocities. Geomorphic effects become stronger with increasing shear stress and with rotors deployed up to half of the channel width, resulting in mean flow distortion within the channel cross section and inducing an alternating scour-deposition pattern resembling the signature of steady, forced fluvial bars. Non-local effects can be mitigated, narrowing the turbine array, or amplified, distributing turbines in a vane-like installation, leading to different estimates of energy production averaged at the power plant scale. A discussion on the key quantities governing geomorphic effects and the potential benefits of asymmetric turbine deployments is provided as a preliminary guideline towards the expansion of Marine Hydrokinetic energy in rivers.