[3] After the outbreak of the Mexican War, Clitz transferred to the bomb brig USS Hecla in 1847, a ship purchased in 1846 and commissioned in 1847 for service in that conflict as part of the Home Squadron.

Later in 1847, Clitz transferred to the screw steamer USS Petrita – also in the Home Squadron but immobilized in Mexican waters due to mechanical problems – until 1848.

Promoted to lieutenant on 6 April 1851, he had duty with the United States Coast Survey from 1851 to 1852, then was aboard the steam paddle frigate USS Mississippi in the East India Squadron from 1852 to 1855.

[2][3] The American Civil War broke out in April 1861, and Clitz served extensively in operations related to the Union blockade of the Confederate States of America.

[2][5] In a dispatch of 28 January 1865, Rear Admiral David Dixon Porter commended him for his actions at Fort Fisher and recommended him for promotion.