NB Coronado was formed from eight established Navy stations in 1997. The base realignment combined NAS North Island, NAB Coronado, Outlying Field Imperial Beach, Naval Auxiliary Landing Field San Clemente Island, Silver Strand Training Complex, Camp Michael Monsoor Mountain Warfare Training Facility at La Posta, Camp Morena, and Remote Training Site Warner Springs.

Naval Amphibious Base Coronado was commissioned January 1944, to supplement amphibious warfare training - prior to this there was only one amphibious base, on the East US Coast - and was immediately put to use training Marine, Seabee, Army, landing craft, and other shore assault units for island campaigns in the Pacific. The base was partially constructed for shore training, using fill from the San Diego Bay. Training included closely coordinated infantry assaults, with naval artillery shore bombardment, and aviation close air support (using attack aircraft from NAS North Island). Other training included "Frogmen" commando training (later SEAL training), river-patrol "brown-water" training. After the war several streets on base were named for battles won by NAB trained units.

Imperial Beach Field was established in World War One as Ream Field, an aerial gunnery range and practice field for aviators operating at NAS North Island. In the between-wars period, the field was still used for landing and take-off practice, as well as on-land carrier practice. In World War Two, Ream Field was used as an auxiliary field for NAS North Island. After the war Ream Field was decommissioned; in 1951 it was recommissioned, and renamed in 1955 as NAAS Imperial Beach. The city of Imperial Beach had encroached on the field, but the Navy had a requirement for a helicopter training field. NAS Imperial Beach Field called itself the Helicopter Capital of the World. In the 1970s NAS Imperial Beach Field was reassigned under command of NAS North Island, leading to the relocation of all housing and unneeded support buildings and functions.

NALF San Clemente Island was established in 1939 as a training and testing site. During World War Two the Island was used for shore bombardment training and landing craft testing and training. After the war the Island continued use as for bombardment training, and was occasionally used by NOTS China Lake for rocket and missile testing. The site is used to this day for Navy and Marine Corps landing assault training, although to a lesser degree than in the past, partially due to the Island's endangered species. Offshore, the waters around the Island are used for submarine training, and anti-mine training (don't go to watch - it's boring, dangerous, and trespassing). NALF San Clemente Island is the Navy's only all-mode training site, and one of its busiest air spaces and water traffic areas.

Camp Michael Monsoor Mountain Warfare Training Facility at La Posta was recently renamed in honor of Medal of Honor recipient Master-at-Arms Petty Officer Second Class Michael A. Monsoor, a SEAL KIA in Iraq in 2006. The Camp is 50 miles east of NB Coronado.