en تخصصي Special مقاله اصیل Original Article <div style="text-align: justify;">Introduction: Seasonal variation of physicochemical parameters and metal concentrations in water sources can affect the type and density of microorganisms. These microorganisms might include pathogenic bacteria, parasites, and viruses. This study aims to investigate contamination of Nile River water at Greater Cairo sites by examining the type of microbiome, physicochemical characteristics, and heavy metal concentrations.<br> Methods: Nile water samples were seasonally collected and centrifuged, and their total DNA was extracted and amplified by polymerase chain reaction (PCR) for qualitative detection of eubacteria, eukaryotes, and adenoviruses. Heavy metals were analyzed in water samples using an atomic absorption spectrometer.<br> Results: No adenoviruses were detected; 97.92% of the samples were positive for eukaryotes, 93.75% for Gram-positive bacteria, and 6.25% for Gram-negative bacteria. Although iron, cadmium, calcium, and copper concentrations were within permissible limits, lead and zinc exceeded the limits at certain sites, with maxima of 93.4 &mu;g/L and 100 mg/L, respectively. Principal component analysis indicated that eukaryotes and Gram-positive bacteria showed positive correlations with temperature and pH, and negative correlations with Zn, Cd, Ca, and Fe. On the other hand, Gram-negative bacteria were positively correlated with dissolved oxygen, and negatively correlated with temperature, pH, total dissolved solids, and Pb.<br> Conclusion: Nile River water in Greater Cairo may be contaminated with pathogenic bacteria, parasites, and fungi. In addition, the physicochemical characteristics and metal pollution of Nile River water correlated with the microbiome type and density in the investigated sites.</div> Eukaryotes, Gram-positive bacteria, Gram-negative bacteria, Lead, Temperature 1 11 http://ehemj.com/browse.php?a_code=A-10-1-448&slc_lang=en&sid=1 Hanaa M. M. El-Khayat hanaamahmoud5999@gmail.com 100319475328460022167 100319475328460022167 No Environmental Research Department, Theodor Bilharz Research Institute, Giza, Egypt Mohamed A. Shemis mohamedshemis@gmx.com 100319475328460022168 100319475328460022168 No Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute, Giza, Egypt Samah Mamdouh samah_mmdh@yahoo.com 100319475328460022169 100319475328460022169 No Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute, Giza, Egypt Wafaa A. Mohammed wafaaabdulaziz32@gmail.com 100319475328460022170 100319475328460022170 No Environmental Research Department, Theodor Bilharz Research Institute, Giza, Egypt Marwa Tamim A. Abdel-Wareth marwatamim2001@hotmail.com 100319475328460022171 100319475328460022171 Yes Correspondence to: Environmental Research Department, Theodor Bilharz Research Institute, Giza, Egypt