Contamination of water and sediment with pyrethroids and triazoles residues can affect fungal diversity, and hence the aquatic system functioning. The aim of the present study is to investigate the effect of water and sediment contamination with pyrethroids and triazoles on fungal diversity. Water and sediment samples were seasonally collected along 2019 from water bodies representing Gharbeya and Qualubeya governorates. Concentrations of pyrethroids and triazoles were determined, and fungal species in water and sediment samples were molecularly identified. The results indicated that temperature and pH varied according to the season. Permethrin, deltamethrin, lambda-cyhalothrin and esfenvalerate showed the highest pyrethroids concentrations, whereas tetraconazole, tebuconazole and difenconazole were of the highest triazoles concentrations. Aspergillus niger was one of the most frequent species, in addition to Trichoderma capillare, Fusarium oxysporum, Penicillium commune and Penicillium polonicum. Principal component analysis indicated a positive correlation between temperature and different Aspergillus spp., and between pH and each of pyrethroids and triazoles. Moreover, a negative correlation was observed between triazoles and Trichoderma asperellum, Penicillium griseofulvum and Aspergillus fumigatus. In conclusion, contamination of water with pesticides affected fungal diversity. This disturbance in fungal assemblages might result in a reduction of some key organisms, or an increase and emergence of new pathogens. © 2023 Taylor & Francis Group, LLC.