According to Mark Boatner's The Civil War Dictionary (Vintage Books, 1959, revised 1988, p. 801), the Stone Fleets were "small sailing ships loaded with stones that were sunk by the Federal Navy at the entrances of Southern harbors. These did not close the channels to blockade runners, as was hoped, for the ships' timbers were soon destroyed by marine worms, and the stones sank in the mud. Three ships were sunk at Ocracoke Inlet, N.C., 18 Nov. '61; 16 in the main entrance to Charleston Harbor 20 Dec. '61; and 20 in a subsidiary entrance to Charleston Harbor, Maffitt's Channel, on 26 Jan. '62."
In a footnote to this poem, which was first published in Battle-Pieces and Aspects of the War in 1866, Melville notes that "All accounts seem to agree that the object proposed was not accomplished. The channel is even said to have become ultimately benefited by the means employed to obstruct it," and laments the destruction of what newspapers of the day referred to as "once famous ships" sunk to no good end.
"The Stone Fleet"