The mission of the Arsenal during its period was aimed at shipping out all ordnance material and general supplies to other arsenals and military facilities, removing usable equipment, and decontaminating the Arsenal grounds and buildings. In 1961, a study for possible contamination sites at the Arsenal was conducted by the Ordnance Corps Headquarters and identified 16 separate areas of potential contamination (Area 1 through Area 16). Considerable effort was spent in 1961 developing detailed decontamination plans for the Arsenal. The decontamination of the Arsenal grounds and buildings was carried out in 1962 and 1963. Prior to July 1963, Raritan Arsenal personnel supervised the decontamination process. After that, personnel from Letterkenny Army Depot (LEAD) supervised the decontamination process. During the decontamination process, an additional area of contamination was identified by the Arsenal staff, namely Area 17, the property disposal and salvage area. The 17 potential contaminated areas identified by the Army represent a portion of the sites incorporated into the USACE DERP-FUDS remedial investigation of the site. The decontamination process at the Arsenal was completed in October 1963.
In 1964, the GSA sold 2,360 acres of Former Raritan Arsenal land to private ownership. The GSA retained 200 acres of the former Arsenal.