[4][5] After graduation, McCauley continued to serve with the Africa Squadron aboard the United States until January 1848 and then back with the Mediterranean Squadron aboard the USS Constitution from October 1848 until 1851 and the USS Independence from October 1851 to June 1852, when he was released to attend his father's funeral in Alexandria, where the elder McCauley had been serving as the first U.S. consul general to Egypt.

Recently married and expecting his first child, he decided to resign from the Navy effective 19 August 1859 and become a businessman in Saint Paul, Minnesota.

[2][4][5] After the outbreak of the Civil War, McCauley rejoined the navy on 11 May 1861 and was assigned as an acting lieutenant on the USS Flag as part of the South Atlantic Blockading Squadron.

[4][5] In Autumn 1864, McCauley joined the Mississippi Squadron, serving aboard the flagship USS Black Hawk.

In November 1864, he assumed command of the large ironclad gunboat USS Benton with additional responsibility for all operations in the 5th Naval District between Grand Gulf and Natchez.

In June 1865, McCauley participated in the capture of the CSS Missouri, the last operational Confederate ironclad on the Mississippi River.

[4][5] Raised in the Mediterranean region, McCauley developed a lifelong interest in Egyptology which he continued to pursue after his retirement.

His father was a diplomat and former U.S. Navy lieutenant and his uncle Charles Stewart McCauley was a career naval officer who retired as a commodore.

[1][10] Their eldest son Carter Nelson Berkeley Macauley (28 July 1859 – 6 February 1896) was an 1882 Jefferson Medical College graduate and United States Army surgeon.