Natural frequencies estimation of Francis turbines is of paramount importance in the stage of design in order to avoid vibration and resonance problems especially during transient events. Francis turbine runners are submerged in water and confined with small axial and radial gaps which considerably decrease their natural frequencies in comparison to the same structure in the air. Acoustic-structural FSI simulations have been used to evaluate the influence of these gaps. This model considers an entire prototype of a Francis turbine, including generator, shaft, runner and surrounding water. The radial gap between the runner and the static parts has been changed from the real configuration (about 0.04% the runner diameter) to 1% of the runner diameter to evaluate its influence on the machine natural frequencies. Mode-shapes and natural frequencies of the whole machine are discussed for all the boundary conditions tested