The current study aimed to evaluate the effect of hydrocarbon pollution including crude oil and naphthalene on the occurrence and clustering of fungal communities in River Nile samples using microcosm experiments. The obtained data revealed that 22 fungal species related to 9 fungal genera were recovered from hydrocarbon-polluted water. The most common fungal genera recovered from naphthalene and crude oil-polluted water were Aspergillus, Penicillium and Trichoderma. Wherease, the fungal species Penicillium purpurogenum, Trichoderma sp. and Aspergillus niger were recorded in the highest occurrence at the control and the polluted microcosm experiments. The highest fungal diversity indices, number of taxa and individuals, dominance, Simpson index, and Shannon index were recorded in crude oil-polluted water. While the lowest fungal diversity indices were estimated at naphthalene-polluted water. Furthermore, the physio-chemical properties of polluted water samples exhibited obvious correlation and influence on the fungal occurrence during different time intervals compared with the control microcosm experiment. The cluster analysis of isolated fungi showed a noticeable grouping of the fungal communities in the control microcosm experiment compared with the naphthalene and crude oil-polluted microcosm experiment. The current data indicated that the ecological impact of emerged pollutants on fungal communities gives a varied fungal grouping and structures.