design: This study employs shotgun metagenomic sequencing to profile bacterial communities in four freshwater reservoirs across Peninsular Malaysia that serve as sources of drinking water. Environmental DNA was extracted from water samples and sequenced using the Illumina HiSeq X Ten platform with 150 bp paired-end reads. The project aims to comprehensively characterize bacterial taxonomic and functional diversity, identify potential waterborne pathogens and assess the influence of anthropogenic activities on microbial community structure and water quality.