Marine Hydrokinetic (MHK) turbines are a growing area of research in the renewable energy field because tidal currents are a highly predictable clean energy source. The presence of a free surface may influence the flow around the turbine and in the wake, critically affecting turbine performance and environmental effects through modification of the wake physical variables. The characteristic Froude number that control these processes is still a matter of controversy, with the channel depth, the turbine’s hub depth, the blade tip depth and the turbine diameter as potential candidates for a length scale. We use a Reynolds Averaged Navier Stokes (RANS) simulation with a Blade Element Theory (BET) model of the turbine and with a Volume of Fluid model, which is used to track the free surface dynamics, to understand the physics of the wake-free surface interactions. Pressure and flow rate boundary conditions for a channel’s inlet, outlet and air side have been tested in an effort to determine the optimum set of simulation conditions for MHK turbines in rivers or shallow estuaries. Stability and accuracy in terms of power extraction and kinetic and potential energy budgets are considered. The goal of this research is to determine, quantitatively in non-dimensional parameter space, the limit between negligible and significant free surface effects on MHK turbine analysis.