It was established on 1 October 1998 when Navy facilities in the Point Loma area of San Diego were consolidated under Commander, Navy Region Southwest. Naval Base Point Loma consists of seven facilities: Submarine Base, Naval Mine and Anti-Submarine Warfare Command (previously Fleet Anti-Submarine Warfare Command), Fleet Combat Training Center Pacific, Naval Information Warfare Systems Command (NAVWAR), Naval Information Warfare Center (NIWC) Pacific, the Fleet Intelligence Command Pacific and Naval Consolidated Brig, Miramar.
On 1 October 1998, Navy facilities in San Diego's Point Loma area were unified under Commander, Navy Region Southwest. This resulted in the formation of Naval Base Point Loma, which includes seven main sites: Submarine Base, Naval Mine and Anti-Submarine Warfare Command, Fleet Combat Training Center Pacific, Naval Information Warfare Systems Command (NAVWAR), Naval Information Warfare Center (NIWC) Pacific, Fleet Intelligence Command Pacific, and Naval Consolidated Brig, Miramar.