Lake Buluan, the third-largest lake in the Philippines, is renowned for its diverse ecosystem, including various endemic fish species and fish pens dedicated to aquaculture. This study focused on analyzing the microbial community diversity in the lake using metabarcoding of the V3-V4 16S rRNA gene amplicon sequencing on llumina MiSeq platform. A total of six amplicon libraries were created, representing sites inside and outside fishing pens. After quality control and processing 917,192 amplicon sequence variants (ASVs) were obtained. The most abundant ASVs belonged to genera such as Cylindrospermopsis, Sphaerospermopsis, Stenotrophomonas, Vibrio, Anabaena, Microcystis, Serratia, Elizabethkingia and some unidentified genera that belong to phyla Verrucomicrobia, Planctomycetes, Chloroflexi, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria. As assessed by the Shannon index, the microbial community’s alpha diversity was high inside fish pens. In addition, the pH level significantly influences the composition of bacterial communities (BCC), leading to the notable presence of bacteria from the phylum Firmicutes, certain Proteobacteria, and Cyanobacteria. The analysis revealed an increased abundance of bacteria associated with toxin production, antibiotic resistance, and opportunistic pathogens. This poses risks to human health, water quality, and ecological systems. This information may impact fish farming practices in the area. Moreover, the predicted functions of the bacterial communities, analyzed using the PICRUSt algorithm within the Parallel-Meta Suite (PMS), indicated their involvement in metabolism and environmental information processing. Notably, the presence of bacteria involved in xenobiotic biodegradation suggests potential applications in bioremediation, including the breakdown of pollutants, hydrocarbons, and heavy metals.