Water quality is one of the most important issues, especially due to the water scarcity that the world is currently facing. Surface water in Egypt is receiving agricultural, industrial, and municipal effluents. The aim of the present study was to investigate the quality of some water canals in Giza and Gharbeya governorates using abiotic and biotic factors. Physicochemical parameters, snail distribution, and frequency of fungal genera were determined from March 2020 to February 2021. The highest water temperatures were recorded during summer and spring in Giza and Gharbeya governorates, respectively, and of electrical conductivity was observed during winter and summer, respectively. Physa acuta snails were the most abundant in all seasons. Also, Aspergillus sp. was the most frequent amongst all identified fungi during all seasons, except winter in Gharbeya Governorate, where Trichoderma sp. was the most frequent. According to the Shannon-Wiener index, autumn showed the highest diversity of snails and fungi in Giza Governorate. For Gharbeya Governorate, snails' diversity showed the highest equal value in summer and autumn, while that of fungi was in spring. In Giza Governorate, Dissolved oxygen showed a strong positive association with Physa acuta and Aspergillus sp. In Gharbeya Governorate, temperature, electrical conductivity, and total dissolved solids exhibited a strong positive correlation with Aspergillus sp., while they showed negative correlations with Lymnaea natalensis and Bulinus truncatus snails. The relationships between fungal genera and snail species varied according to the governorate. In conclusion, low water quality and global warming might result in a decrease of schistosomiasis and fascioliasis dissemination but also can lead to the incidence of more fungal diseases.