Benjamin Stoddert, the first secretary of the navy and Georgetown resident, proposed that as part of a plan for the establishment of naval facilities up and down the Atlantic coast, a naval hospital be built on the Potomac estuary. Later, when the government proposed that shipbuilding also occur at the Potomac facility, an expert from Annapolis selected this site on the Anacostia River as the best place for both of these operations. Thomas Jefferson selected the famed architect Benjamin Henry Latrobe to design the drydock and the facilities' other buildings; Latrobe's neoclassical gatehouse, completed in 1806, still stands.
Burned during the British invasion in 1814, the Navy Yard was rebuilt and remains the navy's oldest shore facility.