The River Yamuna is the largest tributary of River Ganga. This river is as prominent and sacred as the great River Ganga itself. Deterioration in water quality as a result of discharge of allochthonous and autochthonous sources of pollution into water bodies in increasingly rendering the natural water bodies unsuitable for various beneficial purposes to the mankind, like drinking water source, bathing, navigation, fishing and irrigation. It is observed that, due to over pollution of such sacred rivers, the microbial diversity gets increases which increase the BOD and organic load in the water thus making the water polluted. The study showed that the fungal biodiversity is the result of increasing pollution in river Yamuna and is also variable as per the seasonal and climatic variations.