The station is bounded on the northwest by the Naval Supply Center Cheatham Annex, the Virginia Emergency Fuel Farm, and land owned by the Department of the Interior; on the northeast by almost 14 miles (23 km) of the York River and the Colonial National Historical Park; on the southwest by Route 143 and I-64; and on the southeast by Route 238 and the community of Lackey.

The large Camp Peary, which also has much York River frontage on the northern side of the Virginia Peninsula, is adjacent to the Naval Station.

Before DuPont production started, the Navy acquired the site in August 1918 by presidential proclamation in response to the outbreak of World War I in Europe.

[5] The Navy planned to lay the North Sea Mine Barrage to protect commercial shipping and required an Atlantic Seaboard plant to support the effort.

The Navy selected the DuPont site, about 18 square miles (47 km2) of area near Yorktown, Virginia, as the best location on the East Coast for its mine activities.

It had excellent transportation access, with the main lines of the Chesapeake and Ohio Railway forming one of the boundaries of the Depot, and 5 mi (8 km) of waterfront on the navigable York River.

To make way for the new Mine Depot, the government acquired by eminent domain the property of many landowners along the former Yorktown-Williamsburg Road in nearby Lackey, Virginia.

Assisted by self-educated farmer John Tack Roberts (born c.1860), many of the displaced residents of Lackey negotiated better financial compensation for their properties.

Over the years, the growth and expansion of the Navy's technical requirements and responsibilities have been reflected by corresponding developments at the station to support the Atlantic Fleet and CFFC.

Naval Weapons Station Yorktown hosts 25 tenant commands which include the Navy Munitions Command, the Naval Ophthalmic Support and Training Activity, the Marine Corps Second Fleet Antiterrorism Security Team, NAVSUP Fleet Logistics Center Norfolk detachment, Navy Expeditionary Medical Support Command, Navy Expeditionary Logistics Support Group, Riverine Squadron THREE, Maritime Civil Affairs Squadron TWO, and 19 storefronts.