The upwelling phenomenon plays a vital role within marine ecosystems, transporting essential nutrients from the bottom to the surface and boosting biological productivity. However, the bacterial community structure in upwelling zones along the western coast of India (WCI) is understudied. This research systematically examines bacterial diversity across three seasons—pre-monsoon (PR), monsoon (MN), and post-monsoon (PM)—using next-generation sequencing. Our findings show distinct spatial patterns of bacterial communities in the Arabian Sea and demonstrate that ecological variations influence bacterial distribution in this dynamic environment. During MN, the bacterial community exhibited greater species diversity but lower overall abundance compared to PR and PM. Non-Metric MDS cluster analysis revealed a 78% similarity (at order level) between PR and PM, indicating that MN supports unique bacterial diversity. KEGG analysis showed significant seasonal variations in metabolic functions, with increased functional potential during MN. Additionally, Carbohydrate-Active enZymes (CAZymes) analysis revealed distinct seasonal profiles, among which the GH13 enzymes were the most prevalent glycoside hydrolases during MN, predominantly being sucrose phosphorylase and glucosidase, known for breaking down glucan deposits derived from phytoplankton. The CAZymes profiles supported taxonomic and KEGG pathway findings, reinforcing that microbial communities are seasonally distinct and functionally adapted to changing availability of nutrients.