Projected global increases in population density requires a corresponding increase in the securing and provisioning of water resources. While treated wastewater is a suitable supplementary source of both potable and non-potable water, the supply is vulnerable to proliferations of toxigenic cyanobacteria. The eutrophic conditions at wastewater treatment facilities (WWTFs) promote dense Microcystis blooms that disrupt the treatment process and produce the hepatotoxin microcystin, endangering public health. In closed systems such as WWTFs, it is hypothesised that the onset of a toxigenic Microcystis bloom is induced by the reinvasion of an endogenous seeding community from the benthic sediments under favourable environmental conditions. In this study the pelagic and benthic microbiome of an Australian WWTF was characterised to determine the source of pervasive and biannual toxic Microcystis blooms. Intermittent sampling of the WWTF sediment and surface waters was conducted over a two year period (2018-2020). Microbial community profiles of the two compartments was captured using 16S rRNA amplicon sequencing. 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. Results indicate variation within the community profile of the benthic samples time points. Temporal variation in environmental parameters sustain the dominance of diverse Microcystis ecotypes, leading to the depositing of distinct microbial consortia within the sediment. SIMPER analysis was used to identify the microbial taxa contributing to the greatest changes in community profile. Core microbiome analysis indicated conserved ASVs within the sediment and pelagic compartments. This is suggestive of a migratory transition from the WWTF sediment to the surface waters prior to Microcystis bloom initiation. Validation of the benthic compartment storing a repository of viable cells for Microcystis bloom initiation was conducted using a novel in-vitro cyanobacterial bloom model featuring sediments collected from the WWTF.