The study has been carried out to assess the groundwater quality of Kali river Sub-basin of Aligarh City U.P. India. About 100 water samples were collected during pre monsoon and post monsoon period for the year 2015 and analyzed for Heavy metals (Cu, Cd, Cr, Fe, Mn, Ni, Pb,) to understand their behavior in subtropical fluvial system. The study have shown that there is a considerable variation in the concentration of heavy metal from one sampling station to other which may be due to the variation in the quality of industrial and sewage waste being added to the river at different places. The result are compared with the specification prescribed by the Bureau of Indian standard (BIS) 1993 and World Health organization (WHO) 2004. It is revealed that the concentration of Cr, Cd, Ni, Pb, Fe and Mn is higher than the permissible limit prescribed by the Bureau of Indian standard (BIS) 1993 and World Health organization (WHO) 2004. The Heavy industrialization and the increasing urbanization are responsible for the rapidly increasing stress on the ground water of the area. The enormous quantity of waste water generated from domestic, commercial, industrial and other source has led to the problem of ground water in and around Aligarh City, and as in surface water of Kali River. It gives a sign of water quality deterioration, so it is necessary to take rational steps to manage water quality in this region before it becomes a crisis, as this will affect the economy and will also lead to various water-borne diseases.