September in Iquitos is the hottest month of the year. In September, the weather in Iquitos is typically hot. Average daily high temperature in September is about 30 degrees above zero. On average, Iquitos has 27 rainy, 2 sunny, and 1 partly 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 Iquitos.