The water polo pool at the aquatics centre will be drained after it was revealed that an unauthorised dump of 80 litres of hydrogen peroxide was responsible for turning two pools a murky green colour.
The diving pool in the Maria Lenk Aquatics Centre also turned dark green last week, the UK Independent reports.
Organisers had said the water was still safe to enter, although a number of water polo players - competing in the pool alongside the diving one - reported to be suffering from itchy eyes.
The addition of hydrogen peroxide neutralised the chlorine in the pools and meant that algae was able to bloom.
A spokesman for Rio 2016 lamented the ordeal, calling it an 'embarrassment".
It is only the water polo pool that will be drained. The diving pool did not cause as many problems for divers and will remain as it is with organisers continuing to treat the water in the hope for it to return to normal later in the week.
On Saturday the UK Independent reported the diving pool had been closed to athletes wishing to train while organisers attempt to turn the water's colour blue again. According a German diver, the pool 'smells of farts'.
It's water turned green last Tuesday, and was closed for maintenance on Friday.