A converted tobacco warehouse, Castle Thunder was widely regarded as an especially rigorous lockup. Used to house political prisoners, spies, and criminals charge with treason, it was considered to be a fearsome place even by Southerners. Even though the inmates were sometimes allowed boxes of medicine and other supplies, the prison guards had a reputation for brutality.

In 1863 the Confederate House of Representatives ordered an investigation into the conduct of the commandant, Captain George W. Alexander. He was accused of "harshness, inhumanity, tyranny, and dishonesty." Alexander was eventually cleared of the charges, partially by citing the hard-bitten character of the inmates as justification for his behavior.

Alexander thought the most difficult prisoners were the "pug-uglies of Baltimore and the wharf-rats of New Orleans." But not just the commandant thought Castle Thunder residents to especially tough, the prisoners themselves reveled in their fearsome reputation.

After Richmond fell in 1865, Union troops continued to use Castle Thunder to house Confederates accused of war crimes.

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