Many of those countermeasures were described in an order from Rear-Admiral John Dahlgren, issued on January 7, 1864:
I have reliable information that the rebels have two torpedo boats ready for service, which may be expected on the first night when the water is suitable for their movement. One of these is the "David," which attacked the Ironsides in October: the other is similar to it.
There is also one of another kind, which is nearly submerged and can be entirely so. It is intended to go under the bottoms of vessels and there operate.
This is believed by my informant to be sure of well working, though from bad management it has hitherto met with accidents, and was laying off Mount Pleasant two nights since.
There being every reason to expect a visit from or all of these torpedoes, the greatest vigilance will be needed to guard against them.
The ironclads must have their fenders rigged out and their own boats in motion about them.
A netting must also be dropped overboard from the ends of the fenders, kept down with shot, and extending along the whole length of the sides; howitzers loaded with canister on the decks and a calcium [light] for each monitor. The tugs and picket boats must be incessantly upon the lookout, when the water is not rough, whether the weather be clear or rainy.
I observe the ironclads are not anchored so as to be entirely clear of each other's fire if opened suddenly in the dark. This must be corrected, and Captain [Stephen C.] Rowan will assign the monitors suitable positions for this purpose, particularly with reference to his own vessel [USS Ironsides].
It is also advisable not to anchor in the deepest part of the channel, for by not leaving much space between the bottom of the vessel and the bottom of the channel it will be impossible for the diving torpedo to operate except on the sides, and there will be less difficulty in raising a vessel if sunk.
Nets, patrolling boats, close-range guns, and spotlights - all components used to counter submarines in later conflicts. While convoy formations were not applicable to station-keeping off Charleston, the orders specified a defensive formation designed to repel attacks. In short, a respectable list of anti-submarine measures. Everything save perhaps some depth charges.
Clearly directed to the skippers of the ironclad vessels, which primarily operated in the main ship channel off Morris Island, the orders did not address those ships operating further out from the harbor mouth on blockade duty. This was a miscalculation. One way to look at the sinking of the USS Housatonic, as the Hunley scored the first submarine victory in history, the Federals suffered the first failure to defend against that weapon. In that light, Dahglren's orders of January 7, 1864 are among the first pages in a long story about countermeasures taken to defeat the submarine.
(Citation from Official records of the Union and Confederate Navies in the War of the Rebellion. ; Series I - Volume 15: South Atlantic Blockading Squadron (October 1, 1863 - September 30, 1864), pages 226-7.)