Cyanobacterial harmful algal blooms (cyanoHABs) threaten human, animal, and ecosystem health and safety through production of toxic secondary metabolites. Microcystis, a cosmopolitan bloom-forming cyanobacterial genus, is well-known for producing hepatotoxic microcystins (MCs), but it can produce many other bioactive cyanopeptides, such as anabaenopeptins (APs), that occur at high levels in blooms. The toxicological and ecological impacts of such co-occurring cyanopeptides in the natural environment remain understudied. Here we evaluated the effects of pure MCs and APs individually and in combination, as well as extracts of Microcystis cultures producing diverse suites of cyanopeptides, including strains with and without MCs and APs, on human lung (A549), kidney (HK2), and liver (Hep-3B) cell viability. Individual MC and AP congeners exhibited a gradient of toxic effects across cell lines; MC-LA caused the most toxic effects, MC-LR had comparable effects to AP-A and AP-B, and MC-RR caused the least toxicity. Combined exposure to MC-LA and AP-B produced dose-dependent synergistic effects across all three cell lines. Microcystis culture extracts significantly reduced cell viability in dose- and Microcystis strain-dependent patterns that could not be explained by microcystin or anabaenopeptin content alone, suggesting a role of other metabolites and their interactions within the mixtures. These findings demonstrate that mixtures of environmentally relevant cyanopeptides can have greater toxic threats than individual compounds and underscore the importance of considering metabolites beyond MCs and their potential interactions in public health, future risk assessments, and management strategies for cyanoHAB-impacted waters.