Quality of the river water and sediments are deteriorating day by day in Indian rivers due to excessive anthropogenic activities and pollutants entering through various sources. Heavy metal loads in the rivers are one such factor that are adding to human health risks as well. In our study we estimated the concentration of the heavy metals (Pb, Mn, Cr and Cd) in river bed and in water at different points of river Ganga as well as at confluence point of Ganga and Varuna rivers. We found that Ganga river in Varanasi is highly loaded with metals (PLI= 6.698) Mean concentration in water follows: Pb 1.29 mg/L, Mn 1.325 mg/L, Cr 0.169 mg/L and Cd 0.161mg/L, which was above than the permissible limits stated by Environment protection agency EPA in drinking water. Randomly seven indigenous species of fishes were collected from the wild and were processed for checking the occurrence of these metals in the tissues such as Gills, Liver and Muscle. In all the seven selected fish species, degree of heavy metal concentration followed liver > gills > muscles. Highest accumulation of Pb was observed in Cyprinus carpio liver (8.86 μg/g) and lowest in Baikari muscles (0.07 μg/g). Total THQ value i.e. hazard index (HI) of metals was calculated for these fish species that are frequently consumed and the data showed HI values in following sequence: C.carpio > O. nilotus > C.punctatus > J.coitor > M.armatus > M.tengara > Baikari. Average HI value for C. carpioand O. nilotus was found above 1 which indicates that intake of heavy metals through these species may cause health hazard for human. Maximum HI was recorded in Carpio, which is highly consumed fish by human, hence may be harmful to them. These findings pose a threat to human population and hence needs regular monitoring of metals in fishes to prevent entry into food chain and its effect on the human beings.