Aquatic ecosystems significantly influence global biodiversity and ecological processes. To unravel the mysteries of microbial communities within these ecosystems, we conducted a comprehensive metagenomic analysis across diverse aquatic habitats in Bangladesh. Our meticulous collection and processing of water samples, coupled with amplicon sequencing targeting the 16S and 18S rRNA genes and rigorous bioinformatics scrutiny provided deep insights into microbial diversity, intricately detailing the taxonomic distribution, community structure, and potential functional roles within the dynamic microbial assemblages. The 18S sequencing data highlighted the dominant eukaryotic group was Stramenopiles in both canal and lake habitats, while Nucletmycea and Chloroplastida were the dominating groups in the pond and marine environment respectively.