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Oxygen vacancies in strontium titanate surfaces (SrTiO _3 ) have been linked to the presence of a two-dimensional electron gas with unique behavior. We perform a detailed density functional theory study of the lattice and electronic structure of SrTiO _3 slabs with multiple oxygen vacancies, with a main focus on two vacancies near a titanium dioxide terminated SrTiO _3 surface. We conclude based on total energies that the two vacancies preferably inhabit the first two layers, i.e. they cluster vertically, while in the direction parallel to the surface, the vacancies show a weak tendency towards equal spacing. Analysis of the nonmagnetic electronic structure indicates that oxygen defects in the surface TiO _2 layer lead to population of Ti ${{t}_{2g}}$ states and thus itinerancy of the electrons donated by the oxygen vacancy. In contrast, electrons from subsurface oxygen vacancies populate Ti e _g states and remain localized on the two Ti ions neighboring the vacancy. We find that both the formation of a bound oxygen-vacancy state composed of hybridized Ti 3 e _g and 4p states neighboring the oxygen vacancy as well as the elastic deformation after extracting oxygen contribute to the stabilization of the in-gap state.