Freshwater is an essential resource in our life as it serves many human requirements including drinking, industrial and agricultural purposes. The aquatic ecosystem was negatively impacted by urbanization and anthropogenic water pollution. Ibuprofen is considered one of the most common pharmaceuticals used worldwide and is discharged into water by different anthropogenic activities, leading to water contamination and consequently affecting biodiversity and microbial communities of aquatic ecosystems. As the principal producers of extracellular enzymes that enable the breakdown of highly polymeric compounds in aquatic environments, fungi play a crucial function in the aquatic ecosystem. The reservoir system's fungal diversity and its mechanism for the breakdown of pharmaceuticals is still greatly unexplored. Using a microcosm experiment, the impact of ibuprofen on fungal diversity was investigated. The obtained results revealed that 26 fungal species related to 16 fungal genera were isolated from water collected from the microcosm experiment. The highest occurrence of fungal species from the control microcosm was recorded for Trichoderma sp. whereas the highest occurrence was recorded for Aspergillus niger recovered from ibuprofen treated ones. Furthermore, it was found that ibuprofen-contaminated water had adverse effects on fungal taxa, individuals, and Simpson and Shannon indexes compared to the control microcosm experiment. whereas, fungal dominance was increased in ibuprofen-polluted water compared to the control. The current study provides a valuable vision for understanding the impact of the emerging pollutant ibuprofen on fungal diversity and clustering in aquatic ecosystems regarding fungal adaptation and their putative role as bioindicators for ibuprofen contamination in aquatic ecosystems.