She arrived Newport News, Virginia, 30 December; but engine and boiler trouble required her to return to the Washington Navy Yard for repairs.

With Mount Vernon, Howquah, and Nansemond, she engaged Confederate ironclad-ram Raleigh, (Flag Officer William Lynch) which had steamed over the bar at New Inlet 6 May to attack the Northern blockaders.

The withering fire from the Union ships caused Raleigh to withdraw toward safety within the harbor, but she grounded and broke her back while attempting to cross the bar at the mouth of the Cape Fear River.

Shortly before dawn 15 May, Kansas ended a two-hour chase by capturing British steamer Tristram Shandy as the blockade runner attempted to escape to sea with a cargo of cotton, tobacco, and turpentine.

On 7 December, while Admiral David Dixon Porter and General Benjamin F. Butler planned joint operations against Wilmington to close that vital Confederate port once and for all, Kansas was one of the Union gunboats which were making blockade-running in that quarter hazardous.

At daylight Christmas Eve, Kansas was part of the huge fleet which formed in line of battle before Fort Fisher and pounded the formidable Confederate works with a furious bombardment.

Although the cannonade drove the staunch Southern defenders from their guns to shelter in bombproofs, transports carrying the Union soldiers did not arrive from Beaufort until too late to launch the assault that day.

The next morning, the ships again opened fire on the forts and maintained the bombardment while troops landed near Flag Pond Battery, north of the main defensive works.

Lt. Aeneas Armstrong of the Confederate Navy later described the effectiveness of the bombardment, "The whole of the interior of the fort, which consists of sand, merlons, etc., was as one 11 inch shell bursting.

Meanwhile, Kansas and the other wooden warships formed in line of battle in close order and shelled Flag Pond Battery and the adjacent woods at 0715.

After cleanup operations in the Wilmington area, Kansas moved to the James River late in February to support General Grant's final drive to Richmond, Virginia.

The day after General Robert E. Lee surrendered at Appomattox Court House, the gunboat was ordered to a station off Cape Henry to prevent the escape of Confederate sympathizers who were reportedly planning to capture vessels in the bay.

The expedition carefully surveyed the narrow neck of land and recorded invaluable scientific information making "many calculations to prove that a ship-canal across the Isthmus of Tehuantepec is not only practicable, but that the obstacles in the way of the canal route are of the most ordinary nature."

She stood out of Halifax 17 September and arrived New York City 21 November after visiting Salem, Massachusetts, and Newport, Rhode Island, en route.

In November, Spanish authorities in Cuba seized arms-running ship Virginius, illegally flying the American flag on the high seas, and summarily shot 53 of her passengers and crew.

Her final year of active service was devoted to cruising in the Caribbean Sea and the Gulf of Mexico, at the time a region of considerable unrest.