Waste water treatment plants are typically designed to involve a three-phase treatment approach. The primary treatment phase targets the removal of solids, while the secondary phase is designed to reduce the concentration of organic material. The proceeding tertiary phase focuses on the elimination of pathogenic microbes before release into receiving waters. Pelagic samples were collected from three ponds at an Australian waste water treatment plant over two treatment cycles (8 weeks) and amplicon sequencing of the 16S rRNA gene was performed allowing for a thorough mapping of the WWTP microbiome to be completed. Sequence reads were processed using QIIME2 and R, where amplicon sequence variants (ASVs) were constructed. Taxonomic assignment of the sediment and pelagic samples was conducted using a trained SILVA classifier of the 16S v1-3 rRNA hypervariable region. The core WWTP microbiome varied between ponds, but was primarily composed of Flavobacteriales, Frankiales, Burkholderiales, Micrococcales and Rickettsiales. Periods of cyanobacterial bloom proliferation was indicated by a significant increase in the relative abundance of Microcystis in the water column. The microbiome of ponds in the secondary treatment phase, i.e. after nutrient reducing interventions were significantly different to that of the pond prior intervention. The efficacy of this intervention is potentially limited to the pond directly receiving this intervention strategy as the observed cyanobacterial microbiome was invariable between Pond 3 (immediately post intervention) and Pond 10, the final treatment pond. Despite a stable microbial composition, indicator species analysis revealed the emergence of different Microcystis strains within each of the treatment ponds.