Promoted to passed midshipman on June 14, 1834, Alden then served at the Boston Navy Yard until he was assigned to the United States Exploring Expedition under Lieutenant Charles Wilkes.

He saw action at Malolo, in the Fiji Islands, on July 26, 1840, in the punitive expedition against the tribe which had murdered Lieutenant Joseph Underwood and Midshipman Wilkes Henry two days before.

After another tour of duty at the naval station at Boston, Alden was assigned to USS Constitution, and circumnavigated the globe in the frigate during her cruise under Captain John ("Mad Jack") Percival.

The outbreak of the American Civil War in the spring of 1861 found Alden in command of the steamer USS South Carolina, in which he participated in the relief of Fort Pickens.

Appointed Chief of the Bureau of Navigation in April 1869 and promoted to rear admiral on June 19, 1871, Alden returned to sea in 1871 with orders to command the naval force on the European Station.

Although placed on the retired list on March 31, 1872, Alden remained on active duty commanding the European Fleet until relieved by Rear Admiral A. Ludlow Case at Villefranche on June 2, 1873.