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Police were advised that a man had gone missing just off Stevensons Island at midday yesterday, while trying to retrieve a drifting boat.
The Police National Dive Squad found the body at 3.30pm today, not far from where the man went missing.
Police said it was expected that the man's name would be released tomorrow after all next of kin has been advised.
The Police National Dive Squad arrived at the lake this afternoon, where they were being assisted by the Harbourmaster.
A shoreline search was also carried out on the island.
Queenstown Lakes Mayor Jim Boult said earlier today that he had heard the man was "youngish".
"It's terrible when things like this happen in the district and everybody I'm sure is thinking about him and his family," Boult said.
Area response manager Senior Sergeant Allan Grindell said yesterday that the man was on Stevensons Island when he swam out to retrieve a drifting boat but then got into trouble.
Another person swam out to help him but that person wasn't able to locate him, he said.
Local vessels and the Coastguard searched for the man yesterday and a helicopter with paramedics on board was also assisting.
LandSAR volunteers were also helping look for the man yesterday.
Police extended their sympathies to the man's family.
The death will be referred to the Coroner.