A metagenomic approach was applied using 454-pyrosequencing data analysis for the profiling of bacterial communities in the brine samples of the water reclamation plant. Some physicochemical characteristics of brine samples were also determined using standard methods. Samples ranged from being lightly alkaline to highly alkaline (pH 7.40 to pH 10.91) throughout the various treatment stages, with the salinity ranging from 1.62 g/L to 4.53g/L and dissolved oxygen concentrations ranging from 7.47 mg/L to 9.12 mg/L. Phenotypic switching was found to occur due to these physicochemical parameters. Microbial diversities increased from those present in Stage I reactor (6 taxonomic groups) to those in Reverse Osmosis stage I (17 taxonomic groups), whereas in the second phase of the treatment, it increased in Stage II clarifier (14 taxonomic groups) followed by a decrease in Reverse Osmosis stage II (7 taxonomic groups). Overall, 7 phyla were detected, apart from many bacterial sequences that were unclassified at the phylum level. The most dominant phylum found was Proteobacteria accounting for 59% of the total sequences. A BLASTn sequence similarity search showed that the majority of the sequences (56%) were homologous to the uncultured bacterial species, underlining the vast untapped bacterial diversity.