She was arrested as a spy.
The charge of espionage was the Confederacy’s official justification for her detention. Whether it was entirely accurate, or whether it reflected Confederate discomfort with a woman in men’s clothing moving through their lines claiming only medical purposes, is a question the evidence does not fully resolve. What is clear is that she was treated as a prisoner of war rather than executed as a spy, which suggests Confederate command-level uncertainty about the right classification.
She was taken to Richmond, Virginia, and imprisoned at Castle Thunder.
Castle Thunder was a former tobacco warehouse on Cary Street that the Confederacy had converted to a prison in 1861, primarily to hold civilian prisoners, political prisoners, and alleged spies — the categories of prisoner who did not fit the relatively organized framework of prisoner-of-war exchanges between the two armies’ regular soldiers. By 1864 it was overcrowded and operated under conditions that weakened its prisoners physically.
Walker spent four months there, from April to August 1864. The conditions affected her health permanently: after her release she received a disability pension for partial muscular atrophy that the Army attributed to her imprisonment, initially $8.50 per month from June 13, 1865, later raised to $20 per month in 1899. The atrophy was a documented physical consequence of a confinement that the pension system eventually formally acknowledged as service-connected injury.
She was exchanged on August 12, 1864 — or August 9 by some accounts, with her Army contract expiring August 23 — in a prisoner exchange for a Confederate surgeon from Tennessee. The exchange mechanism was the standard arrangement between the armies for returning prisoners of war, and the fact that Walker was exchanged as an equivalent for a Confederate surgeon suggests that whatever classification ambiguity had existed at the time of her capture, by the time of her exchange she was being treated as military personnel.