The contamination of water by hazardous and toxic metals is harmful for the human consumption but the effect is even more critical in presence of excessive nutrient (NO3⁻) and antibiotic resistant bacteria. Heavy metal pollution (HPI) is a powerful tool for ranking amalgamated influence of individual heavy metal on the overall water quality and a view of the suitability of surface water for human consumption. The HPI values of both the rivers are within the critical range of 100, thus suggesting no harmful impact of heavy metal contamination so far in the sampling sites. Health Risk Index (HRI) values of Fe, Cu, Ni and Se in the surface water are also ≥1 thus no critical hazard is observed. Two sites in Brahmaputra River were identified with resistant variety of E.coli, moreover, bacteria resisting to tetracycline is an indication of contamination through wastewater and environmental sources.