One month following the outbreak of the War, Ammen was attached to the frigate USS Roanoke and immediately embarked for the Union blockade.
He was aboard, when Roanoke destroyed the Confederate schooner Mary off Lockwood Folly Inlet, North Carolina, in July 1861.
Ammen was appointed commanding officer of newly commissioned gunboat USS Seneca in September that year and took part in the South Atlantic Blockading Squadron.

Ammen then participated in the Battle of Port Royal on November 7, 1861 and was commended for bravery, when he went ashore to hoist the flag over the surrendered forts, and hold them till the army took possession.
He then took part in the actions on the Wilmington River at the end of January 1862 and participated in the capture of several Confederate vessels and the town of Fernandina, Florida.

Upon his promotion to Commander on July 16, 1862, Ammen assumed command of the gunboat USS Sebago, which he commanded only for a brief period.
He was ordered to Washington, D.C. in October 1862 and joined the monitor USS Patapsco, which was just launched.
The Patapsco was commissioned in January 1863 and Ammen joined with her the South Atlantic Blockading Squadron.

He took part in the Naval bombardment of Fort McAllister between January–March 1863 and although Union ships did not capture the fort, commanding admiral Samuel F. Du Pont had the opportunity to test ship's new guns.
Ammen was relieved due to illness in June that year and was on sick leave until September.
He was subsequently attached to the staff of the South Atlantic Blockading Squadron under Rear admiral John A. Dahlgren and served as Dahlgren's aide aboard the USS Philadelphia.
Ammen took part in the Second Battle of Fort Sumter in September 1863.

Ammen became ill again in January 1864 and spent two months with treatment.
He then assumed temporary command of the USS Shenandoah in March that year and served with the North Atlantic Blockading Squadron for one month, before he was appointed Officer-in-Charge of Marine recruits aboard the merchant vessel SS Ocean Queen in May 1864.
His main task was to transport approximately 220 Naval recruits from Aspinwall, Pennsylvania to New York City.
There was also about 500 passengers aboard that vessel.

The recruits were recently transferred from the Army to the Navy as replacements and shortly after the departure from Aspinwall, approximately 30 recruits began planning the plot to seize the ship.
They intended to kill everyone who should oppose them, and the conspiracy included the running of the vessel, after her seizure, on their own account.
The mutineers attacked Captain Tinklepaugh, but he refused to comply and called for Commander Ammen.

Captain Tinklepaugh, who had expected the difficulty and was prepared, aimed his revolver at the head of the one of mutineers leader, and warned him that if he advanced a step further he would lose his life.
Mutineer sprang forward and Tinklepaugh killed him instantly, Ammen subsequently pulled out his revolver and shot another one, who tried to attack him.
The rest of the mutineers then surrendered and Ammen ordered to put them all to the Handcuffs.

In October 1864, Ammen was appointed commander of the USS Mohican and commanded Mohican during the attacks on Fort Fisher in December 1864 and January 1865.
One month following the outbreak of the War, Ammen was attached to the frigate USS Roanoke and immediately embarked for the Union blockade. He was aboard, when Roanoke destroyed the Confederate schooner Mary off Lockwood Folly Inlet, North Carolina, in July 1861. Ammen was appointed commanding officer of newly commissioned gunboat USS Seneca in September that year and took part in the South Atlantic Blockading Squadron.
Ammen then participated in the Battle of Port Royal on November 7, 1861 and was commended for bravery, when he went ashore to hoist the flag over the surrendered forts, and hold them till the army took possession. He then took part in the actions on the Wilmington River at the end of January 1862 and participated in the capture of several Confederate vessels and the town of Fernandina, Florida.
Upon his promotion to Commander on July 16, 1862, Ammen assumed command of the gunboat USS Sebago, which he commanded only for a brief period. He was ordered to Washington, D.C. in October 1862 and joined the monitor USS Patapsco, which was just launched. The Patapsco was commissioned in January 1863 and Ammen joined with her the South Atlantic Blockading Squadron.
He took part in the Naval bombardment of Fort McAllister between January–March 1863 and although Union ships did not capture the fort, commanding admiral Samuel F. Du Pont had the opportunity to test ship's new guns. Ammen was relieved due to illness in June that year and was on sick leave until September. He was subsequently attached to the staff of the South Atlantic Blockading Squadron under Rear admiral John A. Dahlgren and served as Dahlgren's aide aboard the USS Philadelphia. Ammen took part in the Second Battle of Fort Sumter in September 1863.
Ammen became ill again in January 1864 and spent two months with treatment. He then assumed temporary command of the USS Shenandoah in March that year and served with the North Atlantic Blockading Squadron for one month, before he was appointed Officer-in-Charge of Marine recruits aboard the merchant vessel SS Ocean Queen in May 1864. His main task was to transport approximately 220 Naval recruits from Aspinwall, Pennsylvania to New York City. There was also about 500 passengers aboard that vessel.
The recruits were recently transferred from the Army to the Navy as replacements and shortly after the departure from Aspinwall, approximately 30 recruits began planning the plot to seize the ship. They intended to kill everyone who should oppose them, and the conspiracy included the running of the vessel, after her seizure, on their own account. The mutineers attacked Captain Tinklepaugh, but he refused to comply and called for Commander Ammen.
Captain Tinklepaugh, who had expected the difficulty and was prepared, aimed his revolver at the head of the one of mutineers leader, and warned him that if he advanced a step further he would lose his life. Mutineer sprang forward and Tinklepaugh killed him instantly, Ammen subsequently pulled out his revolver and shot another one, who tried to attack him. The rest of the mutineers then surrendered and Ammen ordered to put them all to the Handcuffs.
In October 1864, Ammen was appointed commander of the USS Mohican and commanded Mohican during the attacks on Fort Fisher in December 1864 and January 1865.
Daniel Ammen