The metagenomic data presented herein contains the bacterial community profile of a drinking water supply system (DWSS) supplying O'Kiep, Namaqualand, South Africa. Representative samples from the source (Orange River) to the point of use (O'Kiep), through a 150km DWSS used for drinking water distribution were analysed for bacterial content. PCR amplification of the 16S rRNA V1–V3 regions was undertaken using oligonucleotide primers 27F and 518R subsequent to DNA extraction. The PCR amplicons were processed using the illumina® reaction kits as per manufactures guidelines and sequenced using the illumina® MiSeq-2000, by means of MiSeq V3 kit. The data obtained was processed using a bioinformatics QIIME software with a compatible fast nucleic acid (fna) file. The raw sequences were deposited at the National Centre of Biotechnology (NCBI) and the Sequence Read Archive (SRA) database, obtaining accession numbers for each species identified.