From what i understand is in Ion implantation, the base silicon is bombarded with an ion beam of sorts. A layer of protective material is placed on the base silicon to leave the areas that need to be doped and those that don't need to be doped: the pattern of the IC. The material is then annealed so the ions further diffuse into the silicon. more info:
I couldn't find anything on Diffusion in Water, but on you othe question, some common materials are pure Silicon as the base or substrate, SiO2 for insulation, N dopants are usually phosphorus, arsenic while boron and gallium are typical P dopants. Aluminum for connectors,connections from chip to mounting package may be aluminum or gold.