Two sets of compounds - one containing fluorine atoms - are grafted onto the cellulose fibres of the paper - which make it hydrophobic or "water-fearing."
Fluorine, containing a dense layer of electrons around its nucleus, is the most electro-negative of all atoms. The oxygen atom of a water molecule also has an electron dense negatively charged portion around its nucleus. Fluorocarbon waxes work because the negatively charged fluorine atoms and negatively charged oxygen portion of the water molecule repel each other (like charges repel, such as with the similar poles of two magnets). It is important to remember that fluorocarbons repel liquid water.
We hope that clarifies your query.