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Charleston was designed as the flagship for the Charleston Squadron, but was delayed considerably in completion. Part of this may be related to redesign efforts, and part of it may have to do with material shortages, as records are quite unclear. Certainly she was very near completion with the [[Union Bombardment of Fort Sumter]] began in 1863. Records as to her commissioning are disputed: the common view is that she had entered the service by February, 1864, but another source claims she wasn't commissioned until July. There are even some suggestions that she may have been commissioned in 1863, but these are probably least likely. It is possible that she served for some time before formal commissioning, since there were reputedly numerous problems with her engines, which often failed to produce the designed 6 knot speed she had been designed for.
Regardless of her commissioning date, she was certainly flagship of the Charleston Squadron from 1864 to 1865, and helped to defend the city and harass nearby Union warships. When the city seemed likely to fall, ''Charleston'' and the other Charleston Squadron ironclads were burned to prevent their capture.