The body was identified as that of 54-year-old Susan, a nun who teaches at the St. Stephens School in Pathanapuram, about 80 kms from the state capital.
At around 9 am, workers at the Mount Tabor Convent first found blood stains near the well and then saw the body floating inside the well, the police said.
Susan had been teaching at the school for the past 12 years.
Both the school and the Convent, is run by the Kottayam-headquartered Malankara Syrian Orthodox Church.
The cause of the death remains unknown.