The aquatic environment has been contaminated by pyrethroids and triazole pesticide applications, which pose serious health risks to the aquatic ecosystem and human beings. Therefore, the current study aims to evaluate water quality parameters, fungal diversity, and distribution of snails and aquatic plants of certain Egyptian water courses contaminated with pyrethroids and triazole pesticides. Seasonal samples were taken throughout 2021 from different water courses at Giza Governorate and Tanta (Gharbeya Governorate). Qualitative and quantitative surveys showed significant differences in water physical parameters between the two investigated governorates. Deltamethrin, permethrin, Es-fenvalerate, and lambada-cyhalothrin showed the highest pyrethroids concentrations, while tebuconazole, tetraconazole, and difenoconazole were the highest triazole concentrations. Fungal diversity displayed 21 molecularly identified fungal species related to four fungal genera: Aspergillus, Fusarium, Penicillium, and Trichoderma. Penicillium sp. and Aspergillus niger were the most frequent species. Snail diversity recorded 10 and 9 species in Giza and Tanta, respectively. Physa acuta was the most abundant snail. Ten species of aquatic plants were observed in Giza, while six species were observed in Tanta. Specifically, Eichhornia crassipes and Lemna gibba were the dominant species in the two governorates, with the relative abundance (39 and 22%) in Giza and (27 and 23%) in Tanta, respectively. Water quality parameters and seasonal variations could control fungal diversity, snails, and aquatic plant distribution. Different relations between pesticides and biological communities may reflect the ability/inability of certain snails and fungi species to commensalism with pesticide concentrations. Continuous pesticide monitoring is essential for life below water and aligns with SDG14. © The Author(s) 2025.