Advancement in sequencing techniques and transformative progress in metagenomics provides an unprecedented platform for functional and taxonomic characterization of the enormous microbial diversity inhabiting and governing various biochemical processes of the freshwater sources. Metagenomic analysis of freshwater resources has led to the discovery and identification of novel microbial genes and an understanding of how microorganisms mediate energy and carbon. In this study, we report the taxonomical classification of bacterial sequences obtained from 6 dam reservoir sites in Pune city, Maharashtra, India. The analysis was performed using two different alignment tools: BLAST and Kaiju. The bacterial diversity was dominated by the presence of Vogecella indigofera, uncultured Proteobacterium, Wolinella Succinogenes, Chromobacterium violaceum, and Heliobacter billis. It was further observed that, despite an identical bacterial composition over various reservoir sites, there were nominal differences in the relative abundance of the inhabitant species. Almost all reservoirs were dominated by Vogecella indigofera (~29%) and uncultured Proteobacterium (~15%). A seasonal analysis performed using BLAST resulted in a number of species exclusive to the season and the site of their growth. A high proportion of unidentified sequences were also reported which demands sequential identification. The results obtained through BLAST and Kaiju, were significantly different, suggesting inconsistencies and inaccuracies in existing metagenomic reads comparison.