The man disappeared off Altona Beach on Port Phillip Bay this afternoon, prompting calls to emergency services about 4pm.
Police divers, two rescue helicopters and lifesavers on boats and jet-skis were seen involved in a widespread search before dark.
The man, who witnesses told police was snorkelling, was last seen towards the east of the Surf Life Saving Club.
Just after 9pm, police confirmed he had been found dead.
Police, who were yet to formally identify the man, were preparing a report for the coroner and not treating the death as suspicious.
