In 1783, Stoddert established a tobacco export business in Georgetown, with business partnersUriah Forrest and John Murdock. After George Washington was elected President, he asked Stoddert to purchase key parcels of land in the area that would become the nation's capital, before the formal decision to establish the federal city on the banks of the Potomac drove up prices there. Stoddert then transferred the parcels to the government. During the 1790s, he also helped found the Bank of Columbia to handle purchases of land in the District of Columbia for the federal government.
In May 1798, President John Adams appointed Stoddert, a loyal Federalist, to oversee the newly established Department of the Navy. As the first Secretary of the Navy, Stoddert soon found himself dealing with an undeclared naval war with France, which would come to be known as the Quasi-War. Stoddert realized that the infant Navy possessed too few warships to protect a far-flung merchant marine by using convoys or by patrolling the North American coast. Rather, he concluded that the best way to defeat the French campaign against American shipping was by offensive operations in the Caribbean, where most of the French cruisers were based. Thus at the very outset of the conflict, the Department of the Navy adopted a policy of going to the source of the enemy's strength. American successes during the conflict resulted from a combination of Stoddert's administrative skill in deploying his limited forces and the initiative of his seagoing officers. Under Stoddert's leadership, the reestablished United States Navy acquitted itself well and achieved its goal of stopping the depredations of French ships against American commerce. Stoddert concerned himself not only with the Navy's daily administration and operations, but also with the service's future strength. He established the first six navy yards and advocated building twelve 74 gunships of the line. Congress initially approved construction of these ships in 1799, and a design was prepared by Joshua Humphrey, who had prepared the initial designs for the 44 gun frigates of 1797 and lumber collected at the new Navy Yards. Following the peace accord with France, the Navy's personnel strength and number of active vessels was reduced. The Jefferson Administration reduced active naval strength to three frigates and sold off or used the collected supplies in the Navy Yards for gunboat construction. This policy left the United States unprepared to respond to the later threats of the Barbary pirates and failed to prevent war with England in 1812. Stoddert established the Navy Department Library as a result of instructions received from President Adams in a letter dated 31 March 1800.
Post-Navy life
He left office in March 1801 to return to commercial life. Following his term as Secretary of the Navy, Stoddert's final years witnessed a decline in his fortunes: as Stoddert lost heavily in land speculation, Georgetown declined as a commercial center, and the Embargo and the War of 1812 brought American overseas trade to a halt. During this period he lived at Halcyon House, on the corner at 3400 Prospect Street NW. Stoddert died on December 13, 1813, and is buried in the graveyard at Addison Chapel, Seat Pleasant, Maryland.
In the Georgetown section of Washington, DC, there was a Stoddert Street named after Benjamin Stoddert. In the Georgetown street renaming of 1895 the name was changed to Q Street NW. An apartment building that today stands at 2900 Q Street NW is named The Stoddert.
