The location houses six key military flag staffs including Commander Third Fleet, US Pacific Fleet, Commanders Carrier Group One and Seven, Commander Naval Air Force, and Commanders Cruiser Destroyer Groups One and Five. Naval Air Station Island is now the most expansive aerospace employer in San Diego.
Included in its facilities are San Clemente Island, Naval Amphibious Base Coronado, Beach and Naval Air Landing Facility, and Outlying Field Imperial. It also has 130 command stations from Coronado to the entrance of San Diego to the Mexico Border. With over 235 aircraft and two aircraft carriers, USS Constellation (CV 64) and USS John C. Stennis (CVN 74), Naval Air Station Island (NASNI) has 23 squadrons and 75 additional tenant commands and activities.
In November 1963 a Navy Submarine Support Facility was established at the San Diego Naval Shipyard as well. Navy downsizing spurred the decommissioning of several command units beginning in April 1995. A final Environmental Impact Statement issued in 1999 resulted in the Navy deciding to upgrade the current facilities and infrastructure at Naval Air Station Island, rather than utilize a different port or build a new one.
Almost a decade later, the San Diego Naval Shipyard was still found to have asbestos. In 2006, tons of asbestos were found with large traces found in 2009 and 2010 throughout various areas of the shipyard. Multiple cleanups have ensued to get rid of the toxin, but workers and family members working at the location were at great risk of developing asbestos diseases from primary exposure and secondary exposure.