September in Manaus is the hottest month of the year. In September, the weather in Manaus is typically hot. Average daily high temperature in September is about 32 degrees above zero. On average, Manaus has 20 rainy, 5 sunny, 4 partly cloudy, and 1 cloudy day in September. The rains are usually heavy. September as well as January, February, March, and April is considered the most uncomfortable time to visit Manaus.