[1] Promoted to master on February 21, 1849[2] and to lieutenant on August 2, 1849,[1][2] Howell returned to sea for a tour aboard the frigate USS Raritan in the Home Squadron from 1849 to 1850.

[1] Howell detached from Minnesota later in 1861 to become the first commanding officer of the new gunboat USS Tahoma, which was commissioned on December 20, 1861, and assigned to the East Gulf Blockading Squadron, with which she remained throughout her career.

[1][2] Tahoma joined the gunboat USS Somerset in putting 111 men ashore in eight boats at Seahorse Key to destroy three Confederate salt works on October 6, 1862.

On June 18, she both captured the British schooner Harrietton off Anclote Key and destroyed the blockade runner Mary Jane at Clearwater, Florida.

On October 17, 1863, she joined the gunboat USS Adela in landing an expeditionary force at Tampa, Florida, and burned the steamer Scottish Chief and the sloop Kate Dale.

[1] Howell's next tour was as the first commanding officer of the schooner-rigged steamer USS Nereus, which was commissioned on April 19, 1864, and assigned to the North Atlantic Blockading Squadron.

Howell and Nereus ended the war searching the Bahamas and the Caribbean for the Confederate States Navy commerce raider CSS Shenandoah.

A French Navy warship got to Santa Cruz first, landed troops, and quelled the rioting there, but not before the rioters had burned the American consulate.

Despite the limited means at Howell's disposal – a squadron consisting of only two ships with which to carry out the responsibility for all U.S. Navy operations off eastern Canada, along the entire United States East Coast and United States Gulf Coast, and in the entire Gulf of Mexico and Caribbean Sea – the Department of the Navy reprimanded him for having neither of his ships ready to deploy to Santa Cruz on short notice and in a timely manner.