The U.S. Navy took control of the former civilian airport in July 1943, purchased an additional 35 acres, and built support buildings and the concrete ramp.

NAAS Watsonville provided training and maintenance for the 12th Naval District, Alameda, California under the Bureau of Yards and Docks, under the command of Lieutenant John C. Chapman.

Also based at the airfield were Grumman TBF Avenger, Vought F4U Corsair and Douglas SBD Dauntless.

Instrument pilots have been advised that Watsonville is occasionally surrounded by non-IFR traffic that climbs or descends to low stratus layers in violation of regulations.

There are frequent radio calls to the common traffic advisory frequency (CTAF), even when instrument meteorological conditions (IMC) prevail.