[1][2] Initially assigned to the sloop USS Hartford on the Asiatic Station, he returned to the United States with the outbreak of the Civil War and served in the gunboat Marblehead during the Peninsular Campaign, March–July 1862; and, afterward, in the blockade of Charleston.

In April 1863, he assumed duties as Executive Officer in the screw sloop Canandaigua and during attacks on Fort Wagner briefly commanded Marblehead.

Following 13 months of imprisonment at Columbia, S.C., Remey was exchanged and returned to duty, serving in the sidewheel steamship De Soto until the end of the war.

Commandant of the Portsmouth Navy Yard at the outbreak of the Spanish–American War, he was ordered to take charge of the Naval Base Key West, whence he directed the supply and repair of all naval forces in Cuban waters and organized supply lines to Army forces in Cuba.

Remey then returned to the United States and served for a year as Chairman of the Lighthouse Board before retiring on August 10, 1903.