The water of river Yamuna caters to diverse needs for the survival of the people. With rapid expansion of industrialization and urbanization the quality of the river is severely affected due to indiscriminate discharge of untreated industrial sludge and some extent to mixing of domestic wastewater with free flowing obnoxious effluents containing multi-level heavy metals, pesticides residue, disinfectants and their byproducts contaminants from the drains into the river which are badly affecting river’s overall ecology. Due to the absence of proper disposal facilities for effluents which directly disposed off onto surrounding land, surface water and even groundwater along the bank of river Yamuna through drains without recommended treatment. As a result of this, hazardous chemicals and metal ions will seep into the groundwater and devastate the water quality across huge areas, and finally leads to serious effects on the health, and the harvest, of the river Yamuna. Hence, the broad concept of healthy river Yamuna ecosystem and lack of proper management needs the research work to assess the concentration level of industrial effluents, distribution and enrichment of contaminated heavy metals which shows their bio-toxic impacts on biodiversity and also highlighted the deterioration of water quality of river Yamuna.