Phosphonic acid-based membranes were prepared by Plasma Enhanced Chemical Vapor Deposition (PECVD) with an input power of 100 W in a continuous or pulsed glow discharge. Comparing both kinds of plasma discharges makes appear that the pulsed configuration gives rise to PECVD materials with longer hydrocarbon chains and thus higher flexible polymer network which consequently present better sorption properties than those prepared from a continuous plasma discharge. Being more hydrophilic and richer in acidic functions than Nafion® 212, PECVD membranes (whatever the kind of plasma discharge, pulsed or continuous, during the deposition of films) present a better water sorption ability. Nevertheless, having a more highly cross-linked structure, they have a lower water diffusion/permeation capacity. Consequently PECVD membranes show singular water management properties which could be a great advantage for the final Proton-Exchange Membrane Electrolyte Cells and Proton-Exchange Membrane Fuel Cells applications.