Hydrogen diffusion is monitored during plasma conditions corresponding to the growth of polymorphous and microcrystalline silicon thin films in the temperature range from 50 to 300 °C. Structural changes of the films were monitored in situ by Spectroscopic Ellipsometry measurements and interpreted with the Bruggemann Effective Medium Approximation along with the Tetrahedron Model. For both materials, diffusion of hydrogen leading to the formation of a hydrogen-rich subsurface layer during the first minute of exposure to the hydrogen plasma is observed. This initial phase was followed by a steady-sate regime during which the thickness of the subsurface layer stayed relatively constant and the total film thickness decreased as a function of time. This steady-state is explained as the result of the equilibrium between hydrogen diffusion and etching. The hydrogen diffusion coefficient and etching rate were calculated from these measurements and found to be higher in amorphous than in polymorphous silicon. This result is consistent with the growth dynamics of polymorphous silicon. It also provides information concerning the nucleation of micro-crystallites in amorphous silicon under very large atomic hydrogen flow conditions. Moreover, it also explains why polymorphous silicon films do not undergo the phase transition to microcrystalline, even if deposited under relatively similar large atomic hydrogen flow conditions.