Unadilla-class gunboats took part in many coastal and river operations, most notably as the bulk of the fleet which captured the vital Confederate port of New Orleans in April 1862.

With the outbreak of the American Civil War in April 1861, the U.S. Navy was faced with an urgent need for light-draft gunboats able to operate both at sea and close inshore to help enforce the Union blockade of Confederate ports.

Six contracts went to New York shipbuilders, five to the State of Maine, four to Massachusetts, three each to Connecticut and Philadelphia, Pennsylvania, and one each to Delaware and Maryland.

[5] The hulls of the Unadilla-class gunboats were designed by Samuel H. Pook, under the direction of the Navy's Chief of the Bureau of Construction, Equipment and Repairs, John Lenthall.

The hulls were strengthened with diagonal iron braces, secured amidships "at the turn of the bilge" and running upward at a 45° angle to the outer frames.

According to Bauer and Roberts, the ships "sailed well in a strong wind and handled easily but rolled badly.

"[3] Gardiner is less generous, describing the vessels as "poor sailors; their machinery frequently broke down; the steering mechanism was inefficient; and they were slow; maximum speed being 8–9 knots.

The following morning, the same three Unadilla-class ships and two other gunboats returned to the harbor to engage the Confederate forts and gauge their strength.

[17] On 7 November, the entire Naval battle fleet, including the three previously mentioned Unadilla-class vessels along with a fourth, USS Unadilla, engaged and defeated the two enemy forts, thus capturing the harbor.

For the operation, Captain David Farragut, Commander of the West Gulf Blockading Squadron, assembled a fleet of 17 warships including nine Unadilla-class gunboats: Cayuga, Itasca, Katahdin, Kennebec, Kineo, Pinola, Sciota, Winona and Wissahickon.

[19] On the night of April 20, Farragut despatched three of his Unadilla-class gunboats, Itasca, Kineo and Pinola to remove the chains obstructing the Mississippi River below New Orleans.

Though coming under heavy but inaccurate fire from Forts Jackson and St. Philip, the vessels were able to clear a narrow passage.

On the night of the 24th, Farragut took the bulk of his fleet through the passage, though three of his Unadilla-class gunboats, Itasca, Kennebec and Winona, became entangled in the river obstructions and were forced to turn back.

[21] The capture of New Orleans enabled Naval forces to move further north along the Mississippi to threaten the key Confederate city of Vicksburg.

For example, in June 1862, several vessels of the class were involved in the "run past Vicksburg" to link up with the naval forces of the upper Mississippi, although this action proved to be of little significance.

[22] Vicksburg was however far too well defended to be threatened by the Navy, and defeat of the Confederate forces in this theater of operations was ultimately left to the Army.

[23] The most successful of the Unadillas in this regard were Sagamore, with 21 prizes; Kanawha with 19; Chocura and Penobscot with 13 each; and Owasco and Tahoma with 11 apiece.

[24][25] Sciota was raised and returned to service, but shortly after the war, on 14 July 1865—the day of Lincoln's assassination—Sciota ran onto a mine in Mobile Bay and was sunk a second time.

[22] The last two vessels of the class to see service with the Navy, Aroostook and Unadilla, were transferred to the newly established Asiatic Squadron in 1867 and subsequently employed in the suppression of piracy along the coast of China.

[26][27] In 1869, both Aroostook and Unadilla were condemned as unfit for further service due to rotting hulls—a legacy of their construction with unseasoned timber—and they were sold shortly thereafter.

Unadilla became the merchant Dang Wee and was sunk in a collision off Hong Kong in the fall of 1870; Aroostook's later history, like that of most other vessels of the class, is unknown.