Starting in 1851, he joined the American merchant marine serving as captain of clipper ships, carrying cargo and passengers to the East Asia and San Francisco.

He served on the Mississippi and along the U.S. coast of the Gulf of Mexico and distinguished himself in battles and incidents at Apalachicola Bay, Sabine Pass, Calcasieu River, Camp Bisland and Butte-à-la-Rose, among others.

[1] He and his party captured the senior Confederate officer in the Calcasieu area, gained possession of eight enemy vessels (one of them single-handedly), defeated rebel infantry, burned their encampment, fought off a cavalry attack, destroyed a bridge and stores, and returned safely without a single casualty.

While over five thousand Union troops on twenty transport ships stood by, he was defeated and captured along with 300 men by the opposing rebel force.

The book Sabine Pass: The Confederacy's Thermopylae by Edward T. Cotham (2004) makes numerous references to Crocker for his actions during the naval blockade by the Union Navy.

Despite the efforts of his superiors to obtain his release, Crocker spent 17 months as a prisoner of war, mainly at Camp Ford, in Tyler, Texas.

Crocker ultimately rose to the rank of Acting Volunteer Lieutenant Commander and was cited on three different accounts—gallantry, and meritorious and faithful services—making him the only U.S. Navy officer to win these three distinctions in the Civil War.

Later in his career, he lost his diplomatic post after refusing to contribute to the presidential campaign of the allegedly corrupt James G. Blaine, Governor of Maine and Secretary of State.

At 47 years of age and in weakened health from his many months in prison camp, he decided to leave the United States with his family and two brothers-in-law.