Cellulose-based filter paper was plasma treated for hydrophobicity and the permeation of the coating investigated. A five-layer stack of filter paper was the model porous medium and perfluoromethylcyclohexane (PFMCH) was the model monomer used in this Study. Water-drop-absorption time (time needed for certain size droplet of water to be completely absorbed) was recorded as a measure of coating effectiveness. Video contact angle measurements were used to evaluate surface hydrophobicity and x-ray photoelectron spectroscopy was used to analyse the surface chemistry of each surface in the stack. It is clear that the outer surface of normally hydrophilic filter paper can easily be made hydrophobic by treatment with PFMCII plasma. By adjusting plasma power, pressure and time, a filter paper can be treated to have one side hydrophobic (water repellent) and the other side hydrophilic (water absorbent). The control of coating penetration into inner layers needs more careful study: it is soon that plasma permeation depends to a small extent on plasma power, negligible extent on background pressure, but to a very large extent on treatment time. During initial deposition, both, the water-drop-absorption rate and the contact angle, have exponential relationships with plasma time. It is shown that CF2 and CF3 functional groups are related to hydrophobic behaviour and that the contact angle and water-absorption time can be correlated to the total fluorine concentration on the surface. A very small amount of surface F is needed for hydrophobic behaviour.