After initial investigations by Thurgau cantonal police, the woman's death is being treated as murder, police said in a statement.
The body was discovered near a popular river swimming area by a passer-by who was out walking her dog on Sunday morning.
Speaking to newspaper Blick, she said “The body lay under a checked yellow blanket. The head was under the water.”
She notified police, who cordoned off the area and brought in divers to investigate the scene.
The body was taken to the Forensic Medicine Institute in St Gallen, where initial findings indicated that the woman had been murdered.
The exact circumstances of the crime and the woman's identity have not yet been established.
Police are seeking information about a white car with Konstanz licence plates which was seen in the area on Saturday night.
Anyone with information should call Thurgau cantonal police on 052 728 22 22.