Water pollution in Egypt is increasing over time, with constant supply of pollutant effluents to the water system from several sources. Water samples were collected for hydrochemical analysis during four successive seasons from some irrigation canals and streams of River Nile in Delta region governorates. There are various correlations patterns between fungal communities and physico-chemical parameters. Air and water temperature were major factors that affect fungal distribution. Calcium and magnesium have inverse correlation on fungal diversity. There was no significant correlation of SO₄^2- and NO₂^- with distribution of freshwater fungi. Ammonia and phosphate encouraged fungal growth. Salinity played active role in determining fungal diversity and community composition. Changes in species composition were correlated positively with elevated concentrations of NH₃⁺ , and pH in some governorates.