Abstract: Water fungi and fungus-like organisms as a biological factor of ecological water systems have significant influence on the environment and its modification. Fresh water samples were collected from region of Ganga River in Varanasi district, Uttar Pradesh, India. Three sampling sites which are known as ghats (stairways to the bank) Assi ghat, Rajendra ghat, Harishchandra ghat) were selected for sample collection. The water samples were examined for fungi by plating method culturing Potato dextrose agar medium. The isolated fungal strains were identified by lactophenol cotton blue staining. Results were found that a total of 23 micoflora were found to be dominant at three place of Ganga River in Varanasi District. In all three places maximum number of fungi was recorded in Assi ghat followed by Harishchandra ghat then Rajendra ghat. Aspergillus flavus and Aspergillus niger showed highest 36.75 and 29.50% frequency at Harishchandra ghat and Rajendra ghat. White sterile mycelium and Trichothecium roseum showed lowest 0.23 and 0.45% frequency in Assi ghat.