Objective: Our work focused on accessing the quality and bacterial diversity of rapidly polluted Bhavani river, the mainline water resource of the Kongunadu region. Methods: Water samples were collected from two sites used by the people for routine use. At the sites of analysis, the water displayed physicochemical values far away from the permissible limits of World Health Organization. Samples were subjected to 16s ribosomal DNA (16s rDNA) sequencing and phylogenetic diversity was inferred from PHYLIP software package. Multi-drug resistance (MDR) of the collected strains were determined by antibiotic susceptibility test. Results: Phylogenetic diversity prediction by 16s rDNA gene sequencing method disclosed the presence of two major phyla, Firmicutes (71%) and Proteobacteria (21%) affiliated to different genera (Bacillus, Paenibacillus, Lysinibacillus, Staphylococcus, Pseudomonas, and Acinetobacter). Of the total population, 35% of the isolates represent novel phenotypes. Antibiotic susceptibility test indicated that >60% of the total bacterial strains showed strong resistance to all the antibiotics. The cumulative resistance percentage ranged from 64 to 82 signifying their adaptive nature to MDR. Conclusion: The results signify the urge toward the management of river water pollution to prevent the occurrence of MDR bacteria in river Bhavani. © 2016, Asian Journal of Pharmaceutical and Clinical Research. All rights reserved.