The deputies, from the Horry County Sheriff’s Office, had been told to safely transport the patients to a mental health center in September, as Hurricane Florence drenched the Carolinas. They were not being evacuated from the floodwaters, but being moved from hospitals for further treatment.

One of the patients, Nicolette Green, 43, had schizophrenia and had been committed on the recommendation of her counselor. The other, Wendy Newton, 45, had asked to be taken to a hospital because she thought she was about to have a “spell.” Both women sought out treatment, hoping to feel better, their families said.

Law enforcement officers were assigned to drive them to the mental health center, as is routine under state law. As water levels rose and roads shut down, Mr. Flood and Mr. Bishop “were provided a travel route that was believed to be safe,” a probable cause affidavit said.

But the deputies did not take the path recommended by their supervisors, according to the affidavit. Instead, the authorities said, they took an alternate route, passing through a barricade and driving into floodwaters on Highway 76 in Marion County in northeastern South Carolina.