When Ward returned to sea, he served once more in the Mediterranean and then saw duty off the African coast in interdicting the slave trade. He next served in the West Indies helping to prevent a resurgence of piracy.
Upon his return to the United States, he taught courses in ordnance and gunnery at the Naval School at Philadelphia, Pa. These popular courses were later published as An Elementary Course of Instruction in Ordnance and Gunnery.

On 10 October 1845, the new Naval Academy opened at Annapolis, Md.; and Lt. Ward was a member of the faculty—one of the first line officers to pass along the benefits of his own experience to young midshipmen. One of the most scholarly officers of the Navy of his day, Ward held the office of executive officer (a post which later became that of the Commandant of Midshipmen), with collateral duties as instructor of gunnery and steam engineering.

The advent of the war with Mexico prompted many naval officers and men to seek assignment to ships serving in Mexican waters. Detached from the Academy, Ward took command of Cumberland in 1847 and served in that capacity for the duration of the war. After a period spent waiting for orders, he was given command of steamer Vixen in 1848 and remained in her through 1850.

After intermittent periods awaiting orders and serving at the Washington and Philadelphia Navy Yards, Ward took command of Jamestown and took her to the African coast to hunt down slave ships trafficking in human flesh. During this time, in his off-duty hours, he proceeded to work on another textbook—A Manual of Naval Tactics—a scholarly work which one day would run into four editions after its initial publication in 1859.

In 1860, as war clouds gathered over the United States, Ward served at the New York Navy Yard, where he wrote a popular treatise on steam engineering, entitled “Steam for the Million.” In the spring of 1861, with the Southern states leaving the Union and Confederate forces mounting a siege at Fort Sumter, S.C., Gideon Welles summoned Ward to Washington to plan for a relief expedition for Sumter. Ward volunteered to lead it but opposition, notably from General Winfield Scott (who perceived it as being futile), forced cancellation of the plans.

Ward pressed for front line service, proposing that a “flying squadron” be established in the Chesapeake Bay for use against Confederate naval and land forces threatening that area south of the Union capital. The idea proved acceptable, and the squadron took shape. With steamer Thomas Freeborn serving as Ward’s flagship, the steamers Freelance, Alliance, and three coast survey ships made up the flotilla.

The newly composed unit—later known as the Potomac Flotilla—saw its first action on 1 June, when guns from Ward’s ships silenced Confederate shore batteries at Aquia Creek. On 27 June, Ward sent a landing party ashore to dislodge Southern forces from another battery at Matthias Point, in St. Mary’s County, but encountered heavy resistance. The Federals gave up the attack and retired, under heavy sniper and cannon fire, to their ships.

Sizing up the situation, Ward brought his flotilla in close to the shoreline to provide gunfire support for the returning Union forces. As he sighted the bow gun in his flagship, Thomas Freeborn, Comdr. James Harmon Ward took a bullet in his abdomen and fell to the deck, mortally wounded. He died within the hour, the first officer of the United States Navy killed during the tragic Civil War.