USS Agassiz was borrowed by the Union Navy from the United States Coast Survey during the American Civil War.

On 30 December 1861, she was ordered to Sag Harbor at the end of Long Island, New York, and served as a revenue cutter at that port into the spring of 1862.

Alexander Murray, the senior naval officer in the sounds of North Carolina, praised "the efficient service rendered by Lieutenant Commanding Robert H. Travers, of the U. S. revenue cutter Agassiz ...The gallant part taken by that vessel was alike creditable to its commanding officer and serviceable in the repulse of the enemy.

"[citation needed] After the damage the cutter had suffered during the action had been repaired by the Norfolk Navy Yard, Agassiz returned north and arrived at New Bedford, Massachusetts, on 27 July 1863, and she seems to have served there through the end of the Civil War.

She moved to Newport, Rhode Island, on 10 October 1865; and, on 29 December of that year, was ordered to New York City where she was transferred back to the U.S. Coast Survey.