Metaproteomics is an emerging field enabling insights into the complex interplay between microorganisms and their influence on biogeochemical processes. The field is particularly relevant to the study of complex cyanobacterial bloom systems, with the potential to map community-wide molecular distributions during bloom initiation, maintenance and senescence. Metaproteomics was applied to identify environmental and physiological drivers of a cyanobacterial bloom in an Australian wetland. The site is home to a transient flying fox colony whose guano was thought to contribute as a major nutrient source. Sediment and upper-pelagic samples were collected to reflect periods of cyanobacterial proliferation, senescence, and wintering over the course of 1 year. Amplicon-based metagenomics was applied in conjunction with peptide-centric profiling to determine Microcystis and Planktothrix as the major cyanobacterial species during bloom periods. PCR amplification of the biosynthetic gene, mcyE, was performed alongside an ELISA to confirm and quantify dissolved concentrations of the cyanotoxin, microcystin, during warmer months. Protein and peptide-level identifications obtained through LC-MS/MS were used to infer the contribution of ammonia and other nitrogenous substances to bloom maintenance. Communities were investigated in the sediment and upper pelagic space to enable insights into species recruitment and potential contributions to bloom initiation. While this study is ongoing, the preliminary data suggest that nitrogenous compounds in bat guano play an important role in driving toxic Microcystis and Planktothrix blooms in this ecologically important wetland.