design: This study employs 16S rRNA gene amplicon sequencing to profile bacterial communities in eight freshwater reservoirs across Peninsular Malaysia used for drinking water supply. Environmental DNA was extracted from water samples and the V3V4 regions of the 16S rRNA gene were PCR amplified and sequenced using Illumina MiSeq technology. The project aims to characterize microbial diversity, detect potential pathogens and assess the impact of anthropogenic activities on water quality.