Cyanobacterial blooms are an escalating ecological concern driven by eutrophication and climate warming. Bloom-forming cyanobacteria can produce a broad spectrum of bioactive secondary metabolites. Among these, microcystins (MCs) are the most recognised hepatotoxins; however, natural populations of Planktothrix agardhii also synthesise numerous non-ribosomal peptides (NRPs) with poorly understood ecological roles and combined toxic effects. This review demonstrated the role of mixtures of P. agardhii cyanometabolites (oligopeptides and biogenic compounds) in cyanobacterial proliferation, emphasising the rapid evolution of chemotypes. The role of P. agardhii oligopeptides other than MCs in the cyanobacterial toxicity to duckweeds is also discussed. Laboratory experiments indicated that crude extracts containing complex peptide mixtures may inhibit Spirodela polyrhiza growth more strongly than pure MC-LR, suggesting synergistic effects within natural metabolite assemblages. Particular attention is given to variant-specific degradation pathways of MCs within duckweed-associated microbiota. By integrating biochemical, ecological, and microbiological perspectives, this synthesis outlines emerging directions in the study of mixtures of cyanobacterial peptides and other compounds, microbial degraders, and macrophyte-associated bioremediation strategies aimed at mitigating cyanotoxin risks in aquatic environments.