[5] At 19, he was given the command of the ship Jenny, belonging to Peter Schermerhorn, grandfather of Mrs. Astor, and was appointed a lieutenant in the Navy from September 17, 1798.

In a letter dated 21 July, 1802 he was ordered to take command of General Greene for an anticipated deployment to the Mediterranean during the First Barbary War.

[8] On November 6, 1812, Commodore Isaac Chauncey set out on a raiding expedition to intercept the enemy vessels on their return from Fort George to Kingston.

On the morning of Nov. 10th he took a small schooner and burnt it, and chased the Royal George into Kingston harbor, and engaged her batteries for an hour and forty-five minutes, but stood off with night coming up.

The American raiders freed prisoners in jail, made wounded soldiers their captives (on paper), and confiscated British military baggage left there and whatever else they could find.

Winfield and his American force of raiders set fire to barracks, a wood yard, and a storehouse on Gibraltar Point.

Isaac Chauncey and his fleet withdrew back to Sacket's Harbor with the captured ships and 260 prisoners of war.

[16] His letters to the Secretary of the Navy provide perhaps the fullest picture and most candid portrait by a career naval officer of the early yard.

These letters deliver rich detail about the officers and employees, and the problems he encountered making the new yard a viable concern.

Writing November 27, 1807, to the Secretary of the Navy, Chauncey pleads for maintenance funds – "The following things are almost indispensable to promote the public service and for the accommodation of the yard.

Two wells to be sunk, in the yard, with pumps in them, windows in the armory, a horse & cart to transport stores, fill holes about the wharf &c &c The tide ebbs & flows in 24 hours consequently leaving a dampness that must destroy the timber next to the ground very soon There is sufficient for the horse in the yard Six wheel barrows with more other little conveniences which I will hope you will leave to my discretion I will not abuse you're your confidence.

Writing on January 5, 1808, to Secretary of the Navy Robert Smith he explained "Some of them (in consequence of Mr. Buckland having mentioned publicly that twenty three gun boats was to be built) immediately had an idea that we could not do without them and would not go to work.

"[18] In May 1829, while in command of the shipyard, Chauncey led a series of searches for the body of George Washington Adams, who committed suicide by jumping from the deck of the steamship Benjamin Franklin.