A man's body has been discovered in waters opposite the St Kilda Marina as thousands attend the St Kilda Festival less than a kilometre away on Sunday afternoon.

Port Phillip Crime Investigation Unit is on the scene along with Homicide Squad detectives, after a passer-by located the partially-submerged body about 1.20pm.

The man's body was pulled from the water by onlookers before the police arrived.

The waters surrounding St Kilda marina.

His cause of death is yet to be determined and police will prepare a report for the Coroner.

A St Kilda Festival spokeswoman said the incident was outside the festival site and had no connection to the festival.