Background: Fungi are free-living heterotrophic microorganisms, which absorb nutrients for growth and reproduction. The integrated fixed film activated sludge (IFAS) system is a beneficial technology for developing conventional activated sludge plants, which consisted of a wide range of microorganisms. Methods: Twelve wastewater samples were collected from four IFAS sites during 3 days. The samples were prepared for count and identification. The genera of fungi were identified by macroscopic and microscopic features. The physical-chemical analyses were done according to the standard method protocols. To prevent and reduce the growth of bacteria, 0.05 g/l of chloramphenicol was added to the synthetic wastewater. Results: The highest count of fungi with a mean concentration was found in the Aeration tank (149 CFU/ml), whereas the lowest count of fungi was found in the Effluent tank (3.3 CFU/ml). The highest diversity of genera (17) was isolated in the Aeration tank, while the lowest diversity of genera (3) was isolated from the Effluent tank. The results of the physical-chemical tests showed that the average removals of COD, TN, and TP in the IFAS fungal system were 91.76%, 91.43%, and 80.23%, respectively. Conclusions: This study on fungi and their ability in reducing nutrients called attention to the role of the IFAS system and its potential for developing a new biological nitrogen removal technology based on fungal treatment.