Across the state of Amazonas, more than 400,000 people have been affected by flooding, said the state's Civil Defense service, many of whom were evacuated as water levels climbed.
The Rio Negro river was rising by about 3 centimeters (1 inch) a day and on Monday streets in the center of Manaus were already under water, according to city hall.
"The water level is... the third highest in the history of the city. If it continues like this, it will pass the record 2012 flood," said mayoral spokesman Emerson Quaresma.
While rainfall varies from year to year, climate change has brought particularly heavy rainy years and also very dry years that hurt farming, said Philip Fearnside, an ecologist at the National Institute of Amazonian Research in Manaus.
Amazon deforestation may also contribute to long-term changes but does not impact rainfall year to year, he said.