As a cousin of Robert E. Lee, his refusal to join the Confederates' side by remaining loyal to the U.S. demonstrated how the war had divided families.

He was appointed a midshipman in the U.S. Navy in November 1825 and subsequently saw extensive service at sea, including combat action during the Mexican–American War and exploration, surveying, and oceanographic duty.

[1] At the outbreak of the American Civil War in 1861, Lee held the rank of commander and was captain of the sloop-of-war Vandalia[3] in the East Indies, sailing her home on his own initiative to join the blockade of the Southern coast.

The Confederates rebuffed Lee's offer of surrender and ordered civilians to evacuate the river city in view of a naval bombardment which never came.

In September 1863 with some supplies being scarce, the admiral advised the naval station at Wilmington, North Carolina that a single small vessel could be used for patrols of that port.

[7] Acting Rear Admiral Lee transferred to the command of the Mississippi River Squadron in October 1864 and led it to the end of the Civil War in 1865.