[1] Flagler's first Civil War assignment was to teach drill and ceremony and other basic skills to newly raised volunteers in Washington, D.C.

When he arrived at his new post, he found that the vast plans for a massive arsenal complex, conceived by his predecessor, General Thomas J. Rodman, had gotten no further than the preliminary stages.

Flager not only developed and completed the major portion of Rodman's great enterprise, but he also authored a highly respected history of the arsenal and its operations, published in 1877.

His service at Rock Island Arsenal was punctuated by a series of shorter temporary assignments; including, membership on the Board of Heavy Gun Carriages in New York (January–March 1873), special inspection duty at Fort Union Arsenal, New Mexico Territory (September 1880), with the specific assignment of winding down the work of that agency; and finally inspection duty at several posts in California, Texas, and New Mexico, completed in February and March 1883.

Flagler's tenure in Philadelphia was frequently interrupted by a variety of special tasks, including presidency of a board designated to test rifled cannon and projectiles in 1889.

By November 1889, Flagler had begun a tour of nearly thirteen months as commandant of Watertown Arsenal, during which period was promoted to the rank of Colonel in September 1890.

He entered his new duties admirably equipped by reason of his wide experience, but the Congresses of the 1890s were not disposed to grant the appropriations he considered necessary for the maintenance and upgrading of the Ordnance Department.

[23] Clement Arthur Finley Flagler was a career Army officer who attained the rank of Major General as a division commander in World War I.

[24][25] In 1895 Elizabeth Flagler was found guilty of manslaughter after she shot and killed a 15-year-old African American boy, one of several she fired a pistol at when she observed them stealing pears from her father's garden.