Naval Weapons Station Yorktown took over a large area of the historic Yorktown and Williamsburg area for storage and loading of ammunition and weapons for the Navy's Atlantic Fleet. Still located on board Yorktown is Lee House, a private residence built in 1649, no longer used for housing. Running through the station is the Old Williamsburg Road where both American Revolution and Civil War infantry once marched.

In 1918, the DuPont Company had purchased 4,000 acres and built a dynamite plant here right before the start of WWI. Once the war started, the Navy took over the land and turned it into the largest naval installation in the world. Eventually more land was acquired to start the North Sea Mine Barrage and Atlantic Seaboard Plant for the storage, assembly, loading and testing of mines by the Navy. At that time, NWS Yorktown was called Navy Mine Depot, Yorktown.

Today there are nearly 40 tenant commands at Yorktown. These include Naval Munitions Command, Naval Ophthalmic Support and Training Activity, Marine Corps Second Fleet Anti-Terrorism Security Team, and the Fleet Industrial Supply Center Detachment.