This paper discusses the mechanical effect of water on the deformation of silicon monocrystals under nano-indentation with the aid of molecular dynamics analysis. The rigid TIP4P model was used to simulate the interactions between water molecules while the long-ranged non-bonded Lennard-Jones potential was applied for the pairs of unlike molecules. It was found that upon loading water molecules are lodged into the cavities of the silicon substrate, causing subsurface damage. The diamond cubic structure in the indentation zone transforms into an amorphous state with a body-centred tetragonal form (β-silicon) below the indentor. The presence of water significantly reduces the indentor-silicon adhesion that alters the structure of the residual deformation zone after complete unloading.