Mangrove and seaweed ecosystems, as integral components of blue carbon habitats, play pivotal roles in global carbon sequestration and coastal protection, showcasing unique environmental dynamics and biological diversity. This study explores seaweed and mangrove-associated bacterial communities and their functional dynamics in Goa coastal habitats, highlighting their critical ecological roles within blue carbon habitats. Physicochemical analysis revealed contrasting environmental conditions, with the seaweed ecosystem experiencing stable marine influences and the mangrove ecosystem subject to dynamic terrestrial-aquatic interactions. Elevated levels of pathogenic bacteria in both ecosystems indicate significant pollution from anthropogenic activities. Advanced metagenomic techniques, including Illumina’s 16S V3-V4 amplicon sequencing, were employed to assess bacterial diversity. The seaweed ecosystems were predominated by Proteobacteria, Cyanobacteria, and Actinobacteria, crucial for nutrient cycling and organic matter decomposition. In contrast, mangrove ecosystems displayed a more complex microbiota, represented by Firmicutes, adapted to anaerobic conditions. Core microbiome analysis revealed the prevalence of the pathogen Pleurocapsa in seaweeds, suggesting ecosystem health decline, while mangrove microbiomes showed the dominance of genera such as Bacillus and Clostridium, which are key in processing organic material under low-oxygen conditions. Notably, Clostridium levels indicated faecal contamination, underscoring the impact of external pollution. Functional pathway analysis conducted with PICRUSt2 analysis elucidated the metabolic specializations of the microbiomes. Seaweed-associated microbiomes excelled in carbohydrate metabolism, cellular growth and death and environmental information processing, whereas mangrove microbiomes showed advanced capabilities in carbohydrate metabolism, xenobiotics biodegradation and complex organic compound metabolism such as terpenoids and polyketides, reflecting complex microbial dynamics and pollution in mangroves. The findings emphasize the urgent need for effective conservation strategies to protect these vital ecosystems against the rising threats of anthropogenic pressures pollution, and climate change. An enhanced understanding of microbial dynamics and functional capabilities is essential for implementing informed management practices, ensuring the conservation and restoration of these critical blue carbon ecosystems.