Emergency services were joined by the RAF and the Coastguard in searching for the trio along the River Tyne near Riding Mill in Northumberland after they failed to return home on Sunday.
Two of them were brothers, aged 41 and 40, and the third was their cousin, aged 36, all from South Shields, South Tyneside.
Northumbria Police said an investigation into the circumstances surrounding their deaths would now begin and a report would be prepared for the coroner.
It is believed the three men had planned their trip and knew the river well, but encountered challenging conditions after heavy rainfall.
After the rescue services received a call at 11pm on Sunday, the first body was recovered from the river by a Sea King helicopter from RAF Boulmer at just after 5.10am and the second body was recovered from the river just before 6.20am in the Corbridge area.
The third body was discovered by officers under the Broomhaugh A68 bridge, yesterday afternoon.
During overnight searches, one of the missing men's vehicles was found at Tyne Green, near to Hexham Rowing Club, just before 1.15am.
A second vehicle belonging to them was found a few hours later, at 4.10am, at Wylam railway station car park and, later on, two kayaks were retrieved.
Chief Superintendent Gordon Milward said: "The weather was unpredictable, in terms of some very heavy showers, and the river was higher than usual and fast-flowing.
"They would be challenging conditions for anybody who decided to go into the water."
Yesterday morning, a green kayak could be seen on the side of the river at Riding Mill pumping station as an RAF Sea King helicopter flew overhead.