The Ganga is a major riverine system of India providing ecosystem services to millions of households. However, this river is under stress due to various anthropogenic activities. River sediment harbours a variety of microorganisms which has a tremendous influence on river health. In the present study, metagenomic approach for microbial community characterization of three sediment samples collected from River Ganga at Farakka stretch was carried out. The sediment samples were sequenced using a high-throughput Next Generation Sequencing platform. Taxonomical classification study showed that the occurrence of bacteria is higher than other groups of microbes. The bacterial classes, such as Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and archaeal phylum, Thaumarchaeota, and Crenarchaeota were relatively higher than other communities. KEGG pathway analysis of three samples revealed that the number of genes associated with environmental information processing is higher in the Lalbag sample in comparison to Farakka barrage and Dhulian samples. The microbial community was categorized by functional classification using SEED analysis. Both COG and SEED analysis revealed that genes associated with carbohydrate metabolism are higher than other functional categories. The genus-level study confirms the higher occurrence of Pseudomonas, which corresponds to anthropogenic activities like mass bathing. The presence of bacterial genus Nitrospira and archaeal phylum Thaumarchaeota confirms a healthy nitrogen cycle in the environment. Moreover, the generated information would help in understanding the importance of microbial communities and their imperative function in maintaining the riverine ecosystem health.