The interaction of water with self-assembled monolayers (SAMs) on amorphous silica is investigated using classical molecular dynamics simulation. Damage is induced through shear simulations with model atomic force microscopy (AFM) tips and separately with controlled extraction. We find that SAM coatings that have been slightly damaged (by normal loads close to 10 nN from a 10-nm-diameter AFM tip) are susceptible to water penetration and migration to the underlying hydrophilic substrate. The controlled damage studies indicate that the presence of water tends to heal damage below a threshold radius and exploits and magnifies damage above this threshold. For the systems studied here, Si(OH)(3)(CH2)(10)CH3 alkylsilane chains on amorphous silica, this threshold radius is between 0.5 and 1.0 nm.