In a letter to Secretary Henry Knox dated 22 October 1794, Humphreys recommended young Doughty for a position as his clerk at the Philadelphia Navy Yard.

The BNC placed such a high value on Doughty's nautical expertise that they scheduled a regular Monday morning meeting to consult with him each week.

[4] The regard he enjoyed with the shipyard workforce also led to considerable tension as during the strike of 1835, when he advised the ship carpenters to hold out for higher wages.

The navy yard payroll for April 1829 shows William Doughty's annual salary as $1,900, nearly the same as a naval captain.

This military unit became known as the "Navy Yard Rifles", becoming a volunteer rifle company that served under the command of Major Robert Brent of the 2nd Regiment of the District of Columbia Militia, who was the first Mayor of Washington, D.C., in the defense of the capital city which resulted in the disastrous defeat in August 1814 at the Battle of Bladensburg.