Tilapia Lake virus and megalocytivirus are two major viruses that are causing global fish declines. The detection of these viruses in nearby water samples suggests a non-invasive and consistent method for identifying fish-viral infections and forecasting early viral illnesses in aquaculture systems. The goal of this study was to examine the prevalence of these viruses in water samples taken from Qarun Lake in Egypt's Fayoum Governorate. 72 water samples were collected regularly from two sites from May 2021 to November 2022. The organic flocculation concentration method was combined with molecular analysis to identify fish viral infections. Only 4.1% of the 72 were infected with tilapia lake virus, whereas 9.7% were infected with megalocytivirus. Finally, our results demonstrated that organic flocculation combined with PCR environmental nucleic acid detection is effective for identifying tilapia Lake virus and megalocytivirus in water.