"If nature is in a bad mood, the probability of problems and garbage is high," he said on Monday, reports Efe.
Moscatelli, who has spent more than two decades working in the Rio de Janeiro area, said that a combination of rain, low tide and a north wind will be bad for water quality in the bay.
High tide and winds blowing from the south, conversely, will push out the garbage and freshen the bay with cleaner Atlantic waters, he said.
International Olympic Committee (IOC) president Thomas Bach said on Sunday that authorities are testing samples from the bay four times a day to ensure the water is compliant with World Health Organisation (WHO) standards.
Moscatelli, however, pointed out that the testing regime cannot guarantee the quality of the water.
"On rainy days and at low tide, the IOC president's comments will collide with reality," the scientist said.
On Monday, four days before the start of the Games, a huge amount of garbage - including tires, bottles and furniture - washed up on the shores of Fundao Island, which sits in Guanabara Bay.
Environmental organisations in Rio de Janeiro are using nets to collect solid waste from the rivers that flow into the bay, but according to Moscatelli, those efforts will be insufficient if weather conditions are unfavourable.
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