Barry, as the Senior Commander of the Navy at the Port of Philadelphia, had charge of the "row gallies, batteries" and other vessels protecting and maintaining the chevaux de frize off Billingsport by sinking obstructions to prevent the passage to the city of any British vessels and thus effectually stopping the channel.

The British erected a battery near the mouth of the Schuylkill upon which Barry's galleys fired at times but seemingly with but little effect, though "playing their part most nobly and acting like men and freemen convincing the world their liberty was merited," to use the words of Thomas McKean to General Rodney.

When, on October 22, 1777, Count Donop attacked the Americans in Fort Mercer at Red Bank, the British fleet coöperated with the land forces, while the Continental vessels under Barry and the Pennsylvania fleet under Hazlewood drove them back, preventing their passage up the river. The British frigate the "Augusta" and the "Merlin" were driven ashore. The "Merlin" was set on fire by its crew. The powder on the "Augusta" exploded and that vessel was blown up. Portions of its remains are in the water off Red Bank to this day.

Fort Mifflin, held by the Americans, was attacked on November 16, 1777. Unable to have the assistance of the Continental or the State Navy, the fort was abandoned. A council of the commanders of the fleet was held, when it was decided that an endeavor should be made at night to take all the vessels up the river, as the British fleet held control of the lower Delaware. To do this it was necessary to pass Philadelphia, then in possession of the British. This was successfully accomplished by the State fleet early in the morning of November 16th. They were "unperceived," says the British account, until the passage had been successfully made. The enemy were more alert the following night when the Continental vessels under Barry endeavored to make the passage. Three or four succeeded. Others had to be burned to prevent capture. The success of this elusive passage up the river emboldened, as we shall see later, Captain Barry, a few months afterwards, to make another successful passage down the river, passing, unmolested, the British vessels off Philadelphia and getting down into the Bay to oppose the British hovering thereabouts.

Barry's operations on the Delaware, while the British occupied Philadelphia, were as brilliant and as audacious in bravery as any services performed during his career. Doubtless from his activity, good judgment and bravery at this period may have proceeded all the successes of his subsequent career. The Continental authorities were made aware at once of the abilities of the gallant man whom they had so early in the struggle for Independence placed in command.

During the attack on Fort Mifflin by the British, Lieutenant Ford, of Barry's "Effingham," and Lieutenant Lyons, of the "Dickinson," deserted. After the British had evacuated Philadelphia these deserters were captured and on September 2, 1778, shot. The execution took place on a guard-boat off Market Street.

After the Continental and State fleets had arrived in the upper Delaware near Bordentown, Washington, in November, 1777, notified the Continental Navy Board there was danger of a British force being sent to destroy the vessels. So he directed they should be sunk. Barry was, by the Board, on November 2d, directed to move the "Effingham" "a little below White Hill" (now Fieldsboro, N.J.) "where she may lie on a soft bottom. You are to sink her there without delay by sunset this evening." But Barry was loath to sink the vessel he had been appointed to command and fight. Later in the month Francis Hopkinson, of the Navy Board, delivered to Captain Barry, as Senior Officer, "orders, in writing," to sink or burn the ships. Captains Barry and Read had taken every measure to defend the vessels which Barry declared he believed would be effectual in repelling any force the enemy would send to destroy them.

Barry and Read protested to the Board against the sinking, saying that if Washington knew the security of the ships he would not order the sinking. Barry offered to go and inform him, but Hopkinson declared Washington had been informed and his order would be carried out. He told Barry that the order should be obeyed; that he would take Washington's opinion in preference to Barry's.

"I told him," related Barry in his defense, when summoned before Congress sitting at York, for disrespect to the Navy Board, "that nevertheless I knew more about a ship than General Washington and the Navy Board together. That I was commissioned by Congress to command the 'Effingham' and, therefore, expected to be consulted before she was destroyed."

"You shall obey our orders," was the quick and somewhat heated reply. Whereupon Barry left him "of course in high dudgeon," said Barry. "I immediately repaired to my ship, got all clear—and the orders were punctually obeyed"—while Hopkinson himself was on board giving orders which did not permit the vessel to keel and so was "very near upsetting." When Barry reported the condition of the ship to the Navy Board, he was told "it was a misfortune and we must do the best to remedy it," to which Barry replied that nothing would be wanting on his part.