The metaproteome profile of a Microcystis bloom-prone wetland in the NSW Hunter region was examined. Samples collected from 2020-2021 were interrogated to track functional responses in the sediment and pelagic communities across 4 seasons. 16S rDNA amplicon and WGS datasets were utilised to demonstrate seasonal taxonomic distribution and generate a blueprint for proteogenomics. Functional terms associated with identified protein groups were used to highlight variability in Microcystis community metabolic processing, showing a preference for specific transporters coinciding with periods of intense cyanobacterial growth. The regulation of nutrient acquisition and cellular compartment proteins in the benthos were also examined and used to help explain potential processes of toxic Microcystis benthic seeding and proliferation during periods of cyanobacterial dominance and senescence. Through functional characterisation of toxic cyanobacterial species in an environmental setting, methods may be suggested for bloom control.