It is argued, on the basis of density functional calculations, that a self-assembled monolayer of oligo(ethylene glycol) or n-alkanes in contact with water will preferentially adsorb hydroxyl ions (either from autoionization of water or added to the solution) on both methoxy- and hydroxide-terminated endgroups, thus charging the surface region of the SAM negatively with an estimated charge density of about 1 muC/cm(2) in agreement with recent experiments. The negative charging can explain long-ranged forces between opposing SAM surfaces. On dense SAMS, hydroxyl ions are highly mobile. Hydronium ions can absorb by penetration into the SAM provided there is enough lateral space for their encapsulation. The important role of hydration is demonstrated by calculating the excess binding energy of adsorption using a Born-Haber cycle.