An unusual conducting surface state can be produced in SrTiO(3) substrates by irradiation with Argon ions from a plasma source, at low energy and high doses. The effects of irradiation are analyzed here by atomic force microscopy (AFM) and aberration corrected scanning transmission electron microscopy (STEM) combined with electron energy loss spectroscopy (EELS). Depth sensitive studies demonstrate the existence of a heavily damaged surface layer and an oxygen vacancy rich layer immediately underneath, both induced during the irradiation process. We find a clear dependence of the Ti oxidation state with the depth, with a very intense Ti(3+) component near the surface. Oxygen vacancies act as n-type doping by releasing electrons into the lattice and producing an insulator-to-metal transition, which explains the unusual metallic behavior of these samples.