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The man, who has not been named, was found unresponsive in the water after recovering an overturned raft during a Queenstown Rafting trip about 11am.
General manager Luke Taylor said in a statement the guide was "well loved and highly respected".
"We are all devastated and staff have been offered support."
The man was one of three guides accompanying 11 passengers on two rafts between Deep Ck, in Skippers Canyon, and Arthurs Point.
The incident occurred just after he went through a rapid in the `Mother' section of the river, about half way through the trip.
"Whilst recovering an overturned raft, he spoke to the dedicated safety kayaker shortly before he was found unresponsive in the water.
"Extensive CPR was performed at the scene, including the use of a portable defibrillator until paramedics arrived, but he did not survive."
The man's body was flown from the site by a Lakes District Air Rescue Trust helicopter soon after midday.
Mr Taylor said the company's rafting operations had been suspended, and it would carry out an internal investigation.
The incident was being handled by the police, and Maritime New Zealand and WorkSafe New Zealand had been informed.
Queenstown Rafting, which merged last year with two other companies under the Go Orange brand, claims to be the country's largest white water rafting operator.