Guides describe the Marshall House as a hotel that never quite emptied. Their stories start with the building's hardest years. According to local tellings, the Union hospital of 1864–65 left its mark, and tour accounts add that the building served as a hospital again during Savannah's yellow fever epidemics. The best-known part of the legend comes from the late-1990s restoration. Ghost City Tours reports that workers lifting damaged floorboards downstairs found human bones. The area was briefly treated as a crime scene, and the bones were later believed to be amputated limbs from the Civil War surgery.

Many of the stories involve children. Guests have described laughter and running feet in the halls late at night, the sound of marbles and rubber balls rolling and bouncing, and crying babies, but nobody is there when they open the door. One story is told on nearly every tour. A mother heard her young son playing and chattering in the bathroom, and he came out in tears, saying "the boy" he'd been playing with had bitten him. There was no other boy, but there was a small bite mark on his arm. Ghost City Tours says other guests have told similar stories.

Then there is Mary Marshall herself. Her portrait hangs behind the front desk, and the hotel's lore includes a little girl who pointed at it and told her father she had seen that lady in the hallway. Other guests have reported a lady in white gliding down the corridors, a well-dressed gentleman reading by a window, a woman who haunts the ladies' restroom and sometimes locks a stall, and the clack of an old typewriter near the room once linked to Joel Chandler Harris. There's even talk of a ghostly cat.

The fourth floor has its own reputation. Visitors have reported loud crashes in the hallway in the early morning hours and doorknobs that rattle as if someone is trying to get in. Guests also describe faucets turning on and off, flickering lights, electronics switching themselves on, and voices with no one behind them. The hotel's reputation grew through ghost tours, guest reviews, and a 2005 appearance on the Travel Channel's Haunted Hotels.