Pan American World Airways used the yacht harbor as the California terminal for China Clipper trans-Pacific flights beginning in 1935.

On 1 June 1936, the city of Alameda, California ceded the airport to the United States government a few months before the Army discontinued operations from the field.

Pan American World Airways shifted its terminal to Treasure Island in 1939 for the Golden Gate International Exposition.

The television series MythBusters often conducted vehicle-based experiments on the grounds of the station (referred to on-air as the "Alameda Runway"), due to the extensive safety zone that could be set up around the test site.

For the same reason, this location has been used as a checkpoint for the Bullrun rally race; the lengthy airstrip allowed for the staging of a challenge involving chasing a semi-trailer.

A two-mile freeway loop was constructed on the base for the filming of a lengthy car chase sequence for the movie The Matrix Reloaded.

Alameda Point Community Partners was selected over Catellus and Harbor Bay/Lennar, and signed a two-year exclusive negotiating contract as the property's master developer.

In August 2010, the Alameda City Council voted to terminate the exclusive negotiating agreement with SunCal and halt its proposal for the former Naval Air Station.

Various reasons were cited in the staff report leading up to the vote, including the developer- and city-initiated ballot measure related to the project that was defeated in February 2010 by a margin of 85%.

The largest of the individual locations is the West Beach Landfill which occupies approximately 110 acres (44.5 ha) in the southwestern corner of the base.