The Bay of Bengal, a vital marine ecosystem of the northeastern Indian Ocean, is struggling with growing environmental changes that hamper its ability to compromise its ecological stability and the livelihoods of many communities depending on its resources. Among the other environmental issues affecting the Bay of Bengal, urban trash, industrial discharges, and agricultural runoff severely compromise the health of its marine life. Dealing with these issues calls for a significant awareness of the existing microbial populations, since they are essential for the ecosystems functioning and the resistance against pollution. Understanding the microbial diversity of the Bay of Bengal will enable us to design focused pollution control plans that support sustainable use of its resources and preserve its unique ecosystems. Metagenomics offers unparalleled resolution in dissecting the intricate microbial assemblages inhabiting the Bay of Bengal, thereby identifying key species involved in pollution degradation and enabling targeted bioremediation programs. This approach can allow us to restore the health of the Bay of Bengal ecosystem and raise our capacity to reduce the pollution effects. Moreover, metagenomics-based research on microbial populations can facilitate the development of new biotechnological techniques for ecosystem restoration, enabling the development of targeted monitoring programs. Recent metagenomics studies highlight the importance of Proteobacteria in ecological assessments and pollution control, as they, along with various eukaryotic taxa, form a major part of the microbial consortia in the Bay of Bengal. These results support an increasing amount of research stressing the need to include metagenomics data into policy frameworks for regional sustainable environmental management. This review emphasizes the escalating environmental challenges confronting the Bay of Bengal, with a specific focus on the transformative potential of metagenomics and how it can revolutionize pollution management.