Australia's assistant swimming coach Michael Bohl has called on Olympic officials to clean the warm-up pool to avoid infections.
Swimming begins with four medals on offer on Saturday, but Australia were not impressed as they went through their final preparations.
Assistant coach Michael Bohl pulled his athletes out of the pool on Thursday because the quality of water concerned him.
Instead, the Australians trained in the main competition pool, while officials asked for the training pool to be cleaned to avoid infections.
"That pool looked really cloudy," he told the Sydney Morning Herald.
"Rather than risk eye, ear or any other infection we brought them in here [the main pool].
"It started out nice but for some reason as the morning wore on the water got really soupy in that pool.
"I just asked FINA officials then and they are working on it."
It is the latest in a number of problems for Australia after their arrival in Brazil was delayed by problems with the Olympic village.
However, Bohl was happy with the standard of the main competition pool ahead of the start of the events.
He added: "It's absolutely beautiful, it's pristine."