Estrella, a side wheel steamer, was transferred from the Army to the Navy late in 1862, and commissioned soon after, Lieutenant Commander A. P. Cooke in command.

Assigned to the West Gulf Blockading Squadron, Estrella served throughout the war off Mobile and New Orleans, along the Texas coast, and up the rivers flowing into the Gulf. During the first 13 days of November 1862 she took part in a series of engagements with CSS Cotton and Confederate shore batteries along the Atchafalaya River and Bayou Teche. With her captain serving as commander of the flotilla maintained in Berwick Bay, Estrella led the attack on CSS Queen of the West 14 April 1863. The Confederate ship was set afire by Union gunfire and after 90 of her crew had been rescued, exploded. Four days later, Cooke led his flotilla up the Atchafalaya once more, to attack the batteries at Butte-a-la-Rose. The batteries were captured intact, with the garrison of 60 men and large supplies of ammunition and commissary stores. A Union Army garrison was at once sent up to hold the town, another key point won by the Navy in its continuing campaign to take complete control of coastal areas.

From 3 to 6 May 1863, Estrella sailed up the Red River to join in the attack on Fort De Russy, and during June and July participated in the attacks on Port Hudson which led to its fall on 9 July. Other outstanding events in her very active service included the capture of schooner Julia A. Hedges in Matagorda Bay, Tex., on 6 April 1864 and leading role in the attacks on Fort Powell in Mobile Bay on 5 August 1864. These attacks were made in coordination with the battle of Mobile Bay.

After being repaired at New Orleans in the first 4 months of 1865, Estrella served as flagship of the West Gulf Squadron, continuing to cruise in the Gulf of Mexico and its tributary waters until 30 June 1867, when she sailed for the New York Navy Yard. There she was decommissioned 16 July 1867, and sold 9 October 1867.