During the Mexican-American War he served aboard the 52-gun frigate USS Congress, and took part in John C. Frémont's expedition from Monterey to Los Angeles, and in the capture of Guaymas and Mazatlán.

Parrott was commissioned as commander in 1861 at the beginning of the Civil War, and was involved in the destruction of Norfolk Navy Yard before it could be taken over by the Confederacy.

In the brig USS Perry he captured the Confederate privateer Savannah, for which he received the commendation of the Navy Department.

He commanded the steamer USS Augusta from 1861 to 1863, participating in the battle of Port Royal, and engaged the Confederate rams Palmetto State and Chicora at the time of their sortie from Charleston on January 31, 1863.

Parrot was in command of the monitor USS Canonicus of the North Atlantic squadron in the engagements with the ironclads on the James River in 1864, and in the fights with Howett's battery.