A method of forming a shallow trench isolation (STI) structure wherein the depth of the STI structure has been extended via formation of an underlying silicon oxide region, has been developed. After definition of a shallow trench isolation shape in a top portion of a semiconductor substrate a self-aligned ion implantation procedure is employed to place oxygen ions in portions of the semiconductor substrate exposed at the bottom portion of the shallow trench shape. Growth of a liner layer on the exposed surfaces of the shallow trench shape, or growth of a liner layer followed by anneal procedure, results in activation of the implanted oxygen ions creating the desired silicon oxide region in a portion of the semiconductor substrate underlying the bottom of the shallow trench shape. Insulator filling of the shallow trench shape now results in a deeper STI structure comprised of the insulator filled shallow trench shape and the underlying silicon oxide region.