Despite these efforts, the two forts, which were separated by the three-mile-wide mouth of the sound, were not adequate to withstand the might of the U.S. Navy. A fleet could maneuver between the two positions and largely keep out of range of either. To be effective, the forts needed guns of longer range and larger caliber, which were unavailable so early in the war.

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In addition to the forts, the sound was protected by a paltry Confederate naval flotilla under the command of Commodore Josiah Tatnall. The fleet was made up of three tugs and a converted river steamer, each of which had two or three guns.

The Union fleet left Hampton Roads on October 29 in a tight, well-disciplined formation. Du Pont was concerned about the hard-to-manage size of the flotilla and the various types of vessels and experience of the commanding officers. Nature conspired against the Union commander, for on November 1 the fleet encountered a hurricane-strength storm off Cape Hatteras that scattered the ships. That same day, Confederate Secretary of War Judah P. Benjamin telegraphed Governor Pickens and General Drayton that an enemy fleet was headed for Port Royal. The point of attack was no longer a secret.

On November 2, Du Pont and Wabash arrived off Port Royal–alone. Now the worth of his detailed planning and preparation, as well as the training and professionalism of his ships' commanders, showed their value. The fleet was largely able to reassemble off the inlet to Port Royal Sound in spite of the severity of the recent storm. By November 4 the flotilla had converged, and during the next few days the vessels prepared for combat and moved over the sound's outer sandbar. At the same time, the coastal survey crew attached to the fleet repaired the marker buoys in the mouth of the sound.

As with all plans, some factors were beyond the control of even the best officers. Despite all the preparations, the army invasion force unwisely had placed all of its ordnance and ammunition aboard one ship, Ocean Express. Originally towed by Baltic until the gale, this was the one ship that did not rendezvous with the fleet and arrive off Port Royal. The soldiers would have to land with only 100 rounds each and no field guns. While Du Pont could supply small-arms ammunition from the fleet's stocks, he could not provide the shells needed by the army's field guns. The attack could not be a joint operation as originally envisioned. Gunfire from the ships would have to silence the forts before the troops could land.

Based on a reconnaissance of the forts protecting Port Royal conducted on November 5, Du Pont and his flag captain, C.H. Davis, developed and issued a novel attack plan that involved a double reduction. It was designed to take full advantage of the large expanse of water between the two defending forts, the mobility of steam vessels and the firepower of the vessels themselves, especially the 44-gun Wabash, as well as the continuity of fire provided by such a large fleet. Fort Walker, Du Pont surmised, was the stronger of the Confederate forts, and operations would initially focus on its reduction.

The plan called for two squadrons, or columns, of ships to move into the sound. The main column, made up of the heaviest ships, would move in a line-ahead formation, with Wabash in the van followed by the frigate Susquehanna, the sloops Mohican, Seminole and Pawnee, the gunboats Unadilla, Ottawa and Pembina and the sailing sloop Vandalia, towed by the steamer Isaac Smith, which had lost all of her guns in the storm. The ships would pass the forts, simultaneously firing on both strongholds.

When they were two miles into the sound, they would turn about to the west and south. As the vessels headed back out of the sound along a line taking them closer to Fort Walker, their guns would fire on that strongpoint's weak northern side as well as enfilade its strongest positions facing the water. Already sailing against the incoming tide, Du Pont's ships would slow to a crawl as they passed the fort. At the mouth of the sound they would turn about once more and retrace their previous path past the forts. This pattern would be maintained until the forts were reduced.

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