Qarun Lake represents an important part of Egyptian history; it is surrounded by many wild and urban environments. In this study, water samples were collected from ten different regions, during different seasons in (2020, and 2021). The water samples were analyzed for their physical properties and the concentrations of the possible heavy metals. One Actinobacteria isolate was identified as Streptomyces noursei based on the partial sequencing of 16S rDNA and, six fungal isolates were fully identified as Aspergillus niger, Aspergillus versicolor, Aspergillus terreus, Aspergillus flavus, Aspergillus fumigatus, and Fusarium oxysporum based on the partial sequencing of 18S rDNA. Fortunately, S. noursei showed antifungal efficacy against three of the tested fungal isolates, with the inhibition zones (18, 16, and 19 mm) against A. niger, A. Fumigatus, and F. oxysporum respectively. Different heavy metals were detected in stations 7, 8, 9, and 10. The highest values of Pb, Cu, Zn, Ni, Cd, and Cr were 35.3, 12.5, 56.6, 12.5, 3.21, and 21.5 respectively. The total viable count of fungi (TVFC) varied between 0.7x10² CFU/mL at site 7 and 5.5x10² CFU/mL at site 1. We can conclude that Qarun Lake contains pathogenic fungi as well as actinomycetes with high antifungal activity and that these microorganisms are closely related to the distribution of heavy metals in Qarun Lake water.