The teenager was found dead by the police national dive squad and his death will be referred to the coroner.
"Police extend their sympathies to his family and loved ones," police said in a statement.
It is understood family and members of the public had been combing the area in a bid to find the teen.
The police dive squad was called in to search for the teenage boy missing in the Waikato River. Photo / Watercare
The swimmer's death comes after a shocking start to the New Year in terms of water fatalities that included the death of Kaelah Marlow who died in what's believed to be a shark attack at Bowentown, near Waihī Beach.
On Wednesday, the body of a missing swimmer in Kaikoura was found after she went missing from South Bay around 7.45pm on Tuesday.
Six people have died in water tragedies in the first week of the year. The four latest deaths have happened within 50 hours of each other.
Water safety advocates are sounding a warning that the high number of people enjoying the warmer water could lead to more dramas along our coastlines, as Kiwis flock to beaches and rivers for respite.
Water Safety New Zealand appealed to all people to make wise decisions around water.
"We know Kiwis will continue to enjoy our beautiful waterways as the warm weather continues," spokeswoman Sheridan Bruce said.
"We need everyone to take responsibility and think about water safety.
"While our waterways are our playground, they can be incredibly unforgiving."
Key safety messages included always taking a buddy, swimming between the flags at patrolled beaches, constant active adult supervision of children around water at all times, watching out for rips, and always wearing a lifejacket on boats and while fishing from rocks or net fishing.
