A local fisherman recovered the man's body and returned it to shore.
Police said the dead man was a local. Authorities are working to contact his next of kin.
Kaikoura Coastguard responded to the incident about 9.50am, president John MacPhail said.
He said a local fisherman based on the coast at Waipapa Bay put his boat in the water and helped to locate the man once the helicopter had spotted him.
Mr MacPhail said the local fisherman who helped in the recovery was very good at responding to these sorts of emergencies.
The Kaikoura Coastguard met him back on shore at Waipapa Bay and tried to resuscitate the drowning victim.
A defibrillator was used by the Coastguard medical team to try to revive the man, but they were unsuccessful.
This was one of those unfortunate and sad incidents that Coastguard attended on behalf of the police, Mr MacPhail said.
"It's very traumatic when we have these incidents and especially when they're more close to home with a local."
Ben Judge, from Clarence River Rafting, said his company had no boats on the river today and he did not know who the fisherman was.
"I had no clients on the river ... and it's a shame I didn't because we may have been some use if we were down there with life jackets and a raft."
He said a lot of private fishermen use the river.
"It's not that much of a fishing hot-spot but it is a place where most days there would be people trying to catch."
