Thereafter, much of land surrounding the former seaplane base and Harvard Aviation Field was taken over by the Navy Department for the construction of a new shipyard called the Victory Destroyer Plant.

The Victory Plant, which was owned by the government but operated by the Bethlehem Shipbuilding Corporation, was designed specifically to mass-produce one type of ship, the Clemson-class destroyers.

Up to this point, NRAS Squantum was a seaplane base only, though occasional naval landplane operations were conducted using the airfield at the nearby Dennison Airport.

The greatest expansion efforts on the base took place between 1939 and 1941 when, among other things, three "proper" paved runways were built (in contrast to the earlier "aerodrome" design) and the old Victory Plant Shipyard buildings (many of which had been gutted during a previous fire) were razed.

During the Second World War NAS Squantum served as a maritime patrol as well as a training base for American and British naval aviators.

Regular Navy squadrons VJ-4 and VS-1D1/VS-31 flew anti-submarine patrols over Massachusetts Bay and the Gulf of Maine using Grumman J2F Ducks, Consolidated PBY Catalinas, Vought-Sikorsky OS2U Kingfishers, Douglas SBD Dauntlesses, and Curtiss SB2C Helldivers.

After the war ended, NAS Squantum became an important component of the new Naval Air Reserve Training Command, some of types based there in numbers being Consolidated PBY-5A/6A Catalinas, Curtiss SB2C-5/CCF SBW-4E Helldivers, Vought F4U-4 and Goodyear FG Corsairs, Douglas R4D Skytrains, North American SNJ Texans and Grumman F6F-5 Hellcats.

The CO's SNB made the official last flight from Squantum when aircraft were transferred en masse to South Weymouth, however, an Avenger with maintenance problems became the last plane to actually depart a few days later.

The base's third problem was that it was old and that many of its facilities had been jury-built using scrap materials and re-used structures salvaged from the Victory Plant Shipyard during the depths of the Great Depression when funds were hard to come by.