A San Francisco fire official said the 18 month old was with his twin sister, his mother and a nanny when they went into the hotel to take some pictures.
While inside, the little boy ran off and disappeared before his mother knew it.
He was found about 10 minutes later, not breathing, in the fountain in the hotel's lobby.
The child was given CPR after being pulled from the water and was said to have a pulse by the time he was taken away in an ambulance. The boy remained hospitalized Thursday with life-threatening injuries, police spokesman Officer Albie Esparza said.
San Francisco fire Lt. Mindy Talmadge explained Wednesday night that the fountain is called an "endless fountain" and it includes a wall of water. She said the boy was hidden by that wall.
Bay City News reported investigators were reviewing security video footage at the hotel to make sure there was no foul play involved. Esparza said it appears to have been simply "a tragic accident."