Objectives: Microbial communities in freshwater are pivotal for driving nutrient transformation, bioremediation, and maintaining the health balance of these ecosystems. However, microbial communities in freshwater ecosystems may undergo rapid shifts in composition in response to environmental changes. In some cases, these shifts may signal ecological imbalance. In the tropics like Malaysia, high humidity coupled with high temperatures and seasonal rainfalls creates an even hotter and highly variable environmental conditions that promote microbial proliferation and increase the risk of introducing potentially pathogenic microorganisms from surrounding anthropogenic sources via surface runoff. The current study offers a comprehensive characterisation of bacterial community composition in Malaysian freshwater drinking reservoirs using high throughput 16 S rRNA gene amplicon sequencing. This approach enables bacterial community profiling and supports initial microbial risk assessment in these vital freshwater ecosystems. Data description: State Authorities permitted the collection of water samples from eight freshwater reservoirs within Peninsular Malaysia’s protective zones. The 16 S rRNA gene’s V3-V4 hypervariable region was amplified for next generation sequencing. Raw DNA sequence data in FASTQ format were quality-filtered, adapter-trimmed and processed using a QIIME v1.9.1 based pipeline that integrated standard bioinformatics tools for OTU clustering and taxonomic assignment. Utilising R v3.3.1, statistical analyses and data visualisations were performed on this dataset. Characterising the community structure of bacteria in these important freshwater ecosystems is the first step to working with this dataset.