[N 1] Norton (2003) argues the Penobscot Expedition was a total failure due to poor planning, inadequate training, and timid leadership on the part of Saltonstall.

In April 1762 he was given command of a letter of marque brigantine, the Britannia, with which he made several successful voyages to the West Indies.

When the American Revolutionary War broke out, Saltonstall joined Connecticut's militia, helping to defend New London's harbor.

When the Continental Navy was established, he was given one of the first captain's commissions, based on the recommendation of his brother-in-law Silas Deane, who served on Connecticut's Naval Committee.

He hired John Paul Jones as his first lieutenant, and gave him the responsibility of overseeing the fitting out of the newly acquired ship.

Saltonstall captained Alfred on the Continental Navy's maiden voyage in March 1776, an expedition to Nassau in the Bahamas whose objective was arms and critically needed gunpowder.

After numerous repeated attempts to pass the bar in 1776 and 1777, the Marine Committee gave her command to Elisha Hinman, who successfully floated her into Long Island Sound in August 1779.

[N 2] Command of the land forces accompanying the expedition was given to a relatively inexperienced Massachusetts militia brigadier general, Solomon Lovell.

Other ship captains in the expedition overwhelmingly agreed that a naval assault was too risky without a simultaneous land attack on the British fort, which Lovell refused to provide.

[N 3] He was found guilty at the trial of ineptitude at Penobscot and was dismissed from the Navy as being "ever after incompetent to hold a government office or state post" the following October by the "Committee for Enquiring into the Failure of the Penobscot Expedition" of the Massachusetts General Court which determined that failure of the expedition was primarily the result of the "want of proper Spirit and Energy on the part of the Commodore", that he "discouraged any Enterprizes or offensive [attack] Measures on the part of our Fleet", and that the total destruction of the fleet was occasioned "principally by the Commodore's not exerting himself at all at the time of the Retreat in opposing the Enemies' foremost Ships in pursuit.

Saltonstall returned to Connecticut, and convinced one of his wife's relatives, Adam Babcock, to support him in a privateering venture.